{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1. Download the dataset from https://ptmint.sjtu.edu.cn/data/PTM%20experimental%20evidence.csv into CSV_PATH = \"../data/ptmint_dataset.csv\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 2. Scrape complex names and features from website" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import requests\n", "from bs4 import BeautifulSoup\n", "import time\n", "import os" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Done: AANAT\n", "Done: AATF\n", "Done: ABCG2\n", "Done: ABI1\n", "Done: ABI3\n", "Done: ABL1\n", "Done: ABRAXAS1\n", "Done: ABRAXAS2\n", "Done: ACACA\n", "Done: ACAP1\n", "Done: ACE\n", "Done: ACE2\n", "Done: ACKR3\n", "Done: ACOT4\n", "Done: ACTB\n", "Done: ACTN1\n", "Done: ACTN4\n", "Done: ADAM22\n", "Done: ADD1\n", "Done: ADORA2A\n", "Done: ADRB2\n", "Done: AFAP1L2\n", "Done: AFF1\n", "Done: AGER\n", "Done: AGO2\n", "Done: AGTR1\n", "Done: AHA2\n", "Done: AHCYL1\n", "Done: AHSA1\n", "Done: AIFM1\n", "Done: AIMP1\n", "Done: AIMP2\n", "Done: AIP\n", "Done: AIRE\n", "Done: AKAP1\n", "Done: AKAP12\n", "Done: AKAP13\n", "Done: AKAP5\n", "Done: AKT1\n", "Done: AKT1S1\n", "Done: ALDH1A1\n", "Done: ALK\n", "Done: AMOT\n", "Done: AMOTL2\n", "Done: AMPH\n", "Done: ANPEP\n", "Done: ANXA1\n", "Done: ANXA2\n", "Done: ANXA7\n", "Done: AP2B1\n", "Done: APAF1\n", "Done: APBA2\n", "Done: APBA3\n", "Done: APBB1\n", "Done: APC\n", "Done: APEX1\n", "Done: APPL1\n", "Done: AQP2\n", "Done: AQP5\n", "Done: AR\n", "Done: ARAP3\n", "Done: ARFIP1\n", "Done: ARHGAP17\n", "Done: ARHGAP22\n", "Done: ARHGAP33\n", "Done: ARHGAP35\n", "Done: ARHGDIA\n", "Done: ARHGDIB\n", "Done: ARHGEF2\n", "Done: ARID3A\n", "Done: ARID4A\n", "Done: ARPP19\n", "Done: ARRB1\n", "Done: ARRB2\n", "Done: ASAP1\n", "Done: ASAP3\n", "Done: ASF1A\n", "Done: ATAD5\n", "Done: ATF1\n", "Done: ATF6\n", "Done: ATG32\n", "Done: ATG4B\n", "Done: ATG9A\n", "Done: ATM\n", "Done: ATP5IF1\n", "Done: ATR\n", "Done: ATRIP\n", "Done: ATXN1\n", "Done: ATXN10\n", "Done: AXL\n", "Done: Akap200\n", "Done: BABAM1\n", "Done: BACE1\n", "Done: BAD\n", "Done: BAIAP2\n", "Done: BAIAP2L1\n", "Done: BAK1\n", "Done: BANF1\n", "Done: BAP1\n", "Done: BBC3\n", "Done: BCAR1\n", "Done: BCL10\n", "Done: BCL11B\n", "Done: BCL2\n", "Done: BCL2L1\n", "Done: BCL2L11\n", "Done: BCR\n", "Done: BCR/ABL\n", "Done: BECN1\n", "Done: BEST1\n", "Done: BIK\n", "Done: BIN1\n", "Done: BIRC5\n", "Done: BLM\n", "Done: BLNK\n", "Done: BNIP3L\n", "Done: BORA\n", "Done: BRAF\n", "Done: BRCA1\n", "Done: BRCA2\n", "Done: BRD4\n", "Done: BRF1\n", "Done: BRIP1\n", "Done: BRMS1\n", "Done: BTG1\n", "Done: BTK\n", "Done: BUB1\n", "Done: BUB1B\n", "Done: BUB3\n", "Done: C16orf74\n", "Done: C2orf88\n", "Done: C3AR1\n", "Done: CALD1\n", "Done: CALM1\n", "Done: CAMK2A\n", "Done: CAMKK1\n", "Done: CAMKK2\n", "Done: CARD9\n", "Done: CASP2\n", "Done: CASP7\n", "Done: CASP8\n", "Done: CASR\n", "Done: CASTOR1\n", "Done: CAV1\n", "Done: CAV2\n", "Done: CAVIN1\n", "Done: CBL\n", "Done: CBLB\n", "Done: CBLC\n", "Done: CBX1\n", "Done: CBX4\n", "Done: CBY1\n", "Done: CCAR1\n", "Done: CCAR2\n", "Done: CCDC106\n", "Done: CCDC50\n", "Done: CCDC6\n", "Done: CCDC88A\n", "Done: CCDC88C\n", "Done: CCKBR\n", "Done: CCND1\n", "Done: CCND3\n", "Done: CCNT1\n", "Done: CCNY\n", "Done: CCR7\n", "Done: CD200R1\n", "Done: CD226\n", "Done: CD247\n", "Done: CD274\n", "Done: CD28\n", "Done: CD300LF\n", "Done: CD33\n", "Done: CD36\n", "Done: CD6\n", "Done: CD93\n", "Done: CDC20\n", "Done: CDC25A\n", "Done: CDC25B\n", "Done: CDC25C\n", "Done: CDC26\n", "Done: CDC27\n", "Done: CDC37\n", "Done: CDC42\n", "Done: CDC42EP4\n", "Done: CDC73\n", "Done: CDCA2\n", "Done: CDCA5\n", "Done: CDCA7\n", "Done: CDCP1\n", "Done: CDH1\n", "Done: CDH2\n", "Done: CDH5\n", "Done: CDK10\n", "Done: CDK16\n", "Done: CDK2\n", "Done: CDK5\n", "Done: CDK5R1\n", "Done: CDK5RAP2\n", "Done: CDK6\n", "Done: CDK9\n", "Done: CDKN1A\n", "Done: CDKN1B\n", "Done: CDKN1C\n", "Done: CDKN2A\n", "Done: CDKN2D\n", "Done: CDT1\n", "Done: CEACAM3\n", "Done: CEBPB\n", "Done: CEBPD\n", "Done: CEBPE\n", "Done: CENPA\n", "Done: CENPJ\n", "Done: CENPU\n", "Done: CEP131\n", "Done: CEP192\n", "Done: CEP55\n", "Done: CERT1\n", "Done: CETN1\n", "Done: CETN2\n", "Done: CFL1\n", "Done: CFTR\n", "Done: CGAS\n", "Done: CHEK1\n", "Done: CHEK2\n", "Done: CHKA\n", "Done: CIC\n", "Done: CIITA\n", "Done: CKMT1A\n", "Done: CLASP2\n", "Done: CLDN11\n", "Done: CLDN16\n", "Done: CLDN2\n", "Done: CLDN4\n", "Done: CLIC5\n", "Done: CLIP1\n", "Done: CLOCK\n", "Done: CLSPN\n", "Done: CLTC\n", "Done: CNKSR1\n", "Done: CNR1\n", "Done: COP1\n", "Done: CORO1A\n", "Done: CORO1B\n", "Done: CREB3L3\n", "Done: CREBBP\n", "Done: CRK\n", "Done: CRTC2\n", "Done: CRY2\n", "Done: CRYAB\n", "Done: CSF1R\n", "Done: CSNK1A1\n", "Done: CTBP1\n", "Done: CTDP1\n", "Done: CTLA4\n", "Done: CTNNA1\n", "Done: CTNNB1\n", "Done: CTNND1\n", "Done: CTPS1\n", "Done: CTTN\n", "Done: CUEDC2\n", "Done: CXADR\n", "Done: CXCR4\n", "Done: CYBA\n", "Done: CYLD\n", "Done: Crb2\n", "Done: DAAM1\n", "Done: DAB1\n", "Done: DAB2\n", "Done: DACT1\n", "Done: DAPK1\n", "Done: DAXX\n", "Done: DAZAP1\n", "Done: DAZL\n", "Done: DBN1\n", "Done: DBNL\n", "Done: DCC\n", "Done: DCD\n", "Done: DCK\n", "Done: DCLRE1C\n", "Done: DCTN6\n", "Done: DCX\n", "Done: DDB1\n", "Done: DDR1\n", "Done: DDX19B\n", "Done: DDX3X\n", "Done: DDX41\n", "Done: DDX5\n", "Done: DDX58\n", "Done: DEF6\n", "Done: DEK\n", "Done: DEPTOR\n", "Done: DIABLO\n", "Done: DISC1\n", "Done: DLG4\n", "Done: DMAP1\n", "Done: DNAJC5\n", "Done: DNAJC6\n", "Done: DNMT1\n", "Done: DOC2B\n", "Done: DOCK1\n", "Done: DOCK8\n", "Done: DOK1\n", "Done: DPYSL2\n", "Done: DPYSL5\n", "Done: DRD1\n", "Done: DRD3\n", "Done: DTL\n", "Done: DTNB\n", "Done: DTYMK\n", "Done: DUSP1\n", "Done: DVL2\n", "Done: DYNLL1\n", "Done: DYNLT1\n", "Done: DYRK1A\n", "Done: Drpr\n", "Done: E2F1\n", "Done: ECD\n", "Done: EDC3\n", "Done: EEF2K\n", "Done: EGFR\n", "Done: EGLN2\n", "Done: EHMT2\n", "Done: EIF2AK2\n", "Done: EIF2AK4\n", "Done: EIF4A3\n", "Done: EIF4B\n", "Done: EIF4E\n", "Done: EIF4EBP1\n", "Done: EIF4G1\n", "Done: EIF4G2\n", "Done: ELAVL1\n", "Done: ELK1\n", "Done: ELMO1\n", "Done: EMD\n", "Done: EML4\n", "Done: ENDOG\n", "Done: ENSA\n", "Done: EP300\n", "Done: EPAS1\n", "Done: EPHA2\n", "Done: EPHB1\n", "Done: EPHB3\n", "Done: EPM2A\n", "Done: EPRS1\n", "Done: EPS8\n", "Done: ERBB2\n", "Done: ERBB3\n", "Done: ERBB4\n", "Done: ERCC6\n", "Done: ERRFI1\n", "Done: ESPL1\n", "Done: ESR1\n", "Done: ESR2\n", "Done: ETS1\n", "Done: ETV4\n", "Done: EXO1\n", "Done: EXOC7\n", "Done: EZH2\n", "Done: EZR\n", "Done: F11R\n", "Done: FADD\n", "Done: FAF1\n", "Done: FANCD2\n", "Done: FANCG\n", "Done: FBP1\n", "Done: FBXO31\n", "Done: FBXO4\n", "Done: FBXW7\n", "Done: FCRL6\n", "Done: FEN1\n", "Done: FERMT2\n", "Done: FGF14\n", "Done: FGFR1\n", "Done: FGFR2\n", "Done: FH\n", "Done: FHIP2B\n", "Done: FKBP5\n", "Done: FKFBP\n", "Done: FLII\n", "Done: FLNA\n", "Done: FLT3\n", "Done: FLT4\n", "Done: FNIP1\n", "Done: FOS\n", "Done: FOXL2\n", "Done: FOXM1\n", "Done: FOXN2\n", "Done: FOXO1\n", "Done: FOXO3\n", "Done: FPR1\n", "Done: FSCN1\n", "Done: FTH1\n", "Done: FUNDC1\n", "Done: FUS\n", "Done: FYB1\n", "Done: FYB2\n", "Done: FZD3\n", "Done: FZR1\n", "Done: G3BP1\n", "Done: GAB1\n", "Done: GAB2\n", "Done: GABARAPL2\n", "Done: GAREM1\n", "Done: GAREM2\n", "Done: GARS1\n", "Done: GATA1\n", "Done: GATA2\n", "Done: GATA3\n", "Done: GATAD2B\n", "Done: GBF1\n", "Done: GCH1\n", "Done: GCM1\n", "Done: GEM\n", "Done: GFAP\n", "Done: GFI1\n", "Done: GGA1\n", "Done: GIT1\n", "Done: GJA1\n", "Done: GLI1\n", "Done: GLUD1\n", "Done: GLUL\n", "Done: GMFG\n", "Done: GMNN\n", "Done: GNA11\n", "Done: GOLPH3\n", "Done: GOT2\n", "Done: GPR15\n", "Done: GRB10\n", "Done: GRB14\n", "Done: GRB2\n", "Done: GRB7\n", "Done: GRIN2A\n", "Done: GRIN2B\n", "Done: GRK2\n", "Done: GRN\n", "Done: GSTA4\n", "Done: GSTP1\n", "Done: GTF2I\n", "Done: GTF2IRD1\n", "Done: GUCY1B1\n", "Done: H1-2\n", "Done: H1-4\n", "Done: H2AC11\n", "Done: H2AX\n", "Done: H2AZ1\n", "Done: H2BC3\n", "Done: H3C1\n", "Done: H4C1\n", "Done: HCLS1\n", "Done: HDAC2\n", "Done: HDAC3\n", "Done: HDAC4\n", "Done: HDAC5\n", "Done: HDAC6\n", "Done: HERC2\n", "Done: HIF1A\n", "Done: HIPK2\n", "Done: HJURP\n", "Done: HMGN1\n", "Done: HMOX1\n", "Done: HNRNPA1\n", "Done: HNRNPK\n", "Done: HNRNPL\n", "Done: HNRNPU\n", "Done: HOXA11\n", "Done: HRAS\n", "Done: HRC\n", "Done: HSD17B4\n", "Done: HSF1\n", "Done: HSF4\n", "Done: HSP90AA1\n", "Done: HSP90AB1\n", "Done: HSPA1A\n", "Done: HSPA5\n", "Done: HSPB1\n", "Done: HTR6\n", "Done: HTT\n", "Done: Hmr-1\n", "Done: ID1\n", "Done: ID3\n", "Done: IDH1\n", "Done: IDH2\n", "Done: IFIH1\n", "Done: IFNAR1\n", "Done: IKBKG\n", "Done: IL10RA\n", "Done: IL22RA1\n", "Done: IL4R\n", "Done: IL6ST\n", "Done: IL7R\n", "Done: IL9R\n", "Done: INCENP\n", "Done: INSIG1\n", "Done: INSIG2\n", "Done: IQGAP1\n", "Done: IQGAP2\n", "Done: IRAK1\n", "Done: IRAK4\n", "Done: IRF3\n", "Done: IRS1\n", "Done: IRS4\n", "Done: ISCU\n", "Done: ITCH\n", "Done: ITGB1\n", "Done: ITGB2\n", "Done: ITGB3BP\n", "Done: ITGB4\n", "Done: ITGB7\n", "Done: ITPR1\n", "Done: JAK2\n", "Done: JAK3\n", "Done: JUN\n", "Done: JUNB\n", "Done: JUP\n", "Done: KAT6A\n", "Done: KAT7\n", "Done: KAT8\n", "Done: KCNA2\n", "Done: KCNH2\n", "Done: KCNN4\n", "Done: KCTD12\n", "Done: KDM1A\n", "Done: KDM3A\n", "Done: KDM4C\n", "Done: KDR\n", "Done: KEAP1\n", "Done: KHSRP\n", "Done: KIF13B\n", "Done: KIF22\n", "Done: KIF23\n", "Done: KIF2C\n", "Done: KIF3A\n", "Done: KIR2DL1\n", "Done: KIT\n", "Done: KLC2\n", "Done: KLF10\n", "Done: KLF4\n", "Done: KLF5\n", "Done: KLF8\n", "Done: KLHL3\n", "Done: KLRF1\n", "Done: KMT2A\n", "Done: KPNA2\n", "Done: KPNA4\n", "Done: KRAS\n", "Done: KRT18\n", "Done: KRT19\n", "Done: KRT5\n", "Done: Klp9\n", "Done: L1CAM\n", "Done: L3MBTL2\n", "Done: LAIR1\n", "Done: LARP6\n", "Done: LARP7\n", "Done: LASP1\n", "Done: LCK\n", "Done: LCP1\n", "Done: LCP2\n", "Done: LDHA\n", "Done: LEF1\n", "Done: LEMD3\n", "Done: LEO1\n", "Done: LGALS3\n", "Done: LIG1\n", "Done: LILRB2\n", "Done: LIN52\n", "Done: LMNA\n", "Done: LMNB1\n", "Done: LRP1\n", "Done: LRP6\n", "Done: LRRC4C\n", "Done: LRRFIP2\n", "Done: LRRK2\n", "Done: LSR\n", "Done: LY6G6F\n", "Done: LZTS2\n", "Done: MAD1L1\n", "Done: MAD2L1\n", "Done: MAD2L1BP\n", "Done: MAF1\n", "Done: MAFA\n", "Done: MALT1\n", "Done: MAML1\n", "Done: MAP1LC3A\n", "Done: MAP1LC3B\n", "Done: MAP1LC3C\n", "Done: MAP2\n", "Done: MAP2K1\n", "Done: MAP2K2\n", "Done: MAP2K6\n", "Done: MAP3K1\n", "Done: MAP3K11\n", "Done: MAP3K2\n", "Done: MAP3K3\n", "Done: MAP3K5\n", "Done: MAP3K6\n", "Done: MAP3K7\n", "Done: MAP3K8\n", "Done: MAP4K3\n", "Done: MAPK1\n", "Done: MAPK4\n", "Done: MAPK6\n", "Done: MAPK7\n", "Done: MAPK8\n", "Done: MAPK8IP1\n", "Done: MAPRE1\n", "Done: MAPRE3\n", "Done: MARK2\n", "Done: MARS1\n", "Done: MAVS\n", "Done: MCAM\n", "Done: MCC\n", "Done: MCF2\n", "Done: MCL1\n", "Done: MCM2\n", "Done: MCM7\n", "Done: MCPH1\n", "Done: MCRIP1\n", "Done: MDC1\n", "Done: MDM2\n", "Done: MDM4\n", "Done: ME1\n", "Done: MECOM\n", "Done: MECP2\n", "Done: MED1\n", "Done: MED28\n", "Done: MEF2C\n", "Done: MEF2D\n", "Done: MEFV\n", "Done: MELK\n", "Done: MET\n", "Done: METTL14\n", "Done: METTL3\n", "Done: MEX3B\n", "Done: MFF\n", "Done: MFN2\n", "Done: MIIP\n", "Done: MIP\n", "Done: MISP\n", "Done: MLKL\n", "Done: MLLT1\n", "Done: MME\n", "Done: MMP14\n", "Done: MOB1A\n", "Done: MORC2\n", "Done: MPH1\n", "Done: MPIG6B\n", "Done: MPL\n", "Done: MPLKIP\n", "Done: MRE11\n", "Done: MSN\n", "Done: MST1R\n", "Done: MTHFR\n", "Done: MTOR\n", "Done: MTSS1\n", "Done: MTURN\n", "Done: MUS81\n", "Done: MVB12A\n", "Done: MVP\n", "Done: MYBL2\n", "Done: MYC\n", "Done: MYCN\n", "Done: MYH9\n", "Done: MYL12A\n", "Done: MYL2\n", "Done: MYOD1\n", "Done: MZF1\n", "Done: Mad\n", "Done: Mtor\n", "Done: NABP2\n", "Done: NANOG\n", "Done: NBN\n", "Done: NCAPD3\n", "Done: NCF1\n", "Done: NCOA3\n", "Done: NCOA6\n", "Done: NDD1\n", "Done: NDE1\n", "Done: NDRG1\n", "Done: NEDD1\n", "Done: NEDD4L\n", "Done: NEK7\n", "Done: NEK9\n", "Done: NELFE\n", "Done: NF2\n", "Done: NFAT5\n", "Done: NFATC1\n", "Done: NFATC2\n", "Done: NFE2L2\n", "Done: NFKB2\n", "Done: NGFR\n", "Done: NHEJ1\n", "Done: NIBAN1\n", "Done: NIBAN2\n", "Done: NIFK\n", "Done: NINL\n", "Done: NKX3-1\n", "Done: NLRP3\n", "Done: NOLC1\n", "Done: NOP53\n", "Done: NOS3\n", "Done: NOX4\n", "Done: NOXA1\n", "Done: NPHP1\n", "Done: NPHS1\n", "Done: NPM1\n", "Done: NQO1\n", "Done: NR1I2\n", "Done: NR1I3\n", "Done: NR3C1\n", "Done: NR4A1\n", "Done: NRAS\n", "Done: NRBF2\n", "Done: NRIP1\n", "Done: NSD2\n", "Done: NSF\n", "Done: NSUN2\n", "Done: NTRK1\n", "Done: NUPR1\n", "Done: OCLN\n", "Done: OFD1\n", "Done: OPTN\n", "Done: OSBP2\n", "Done: OSTF1\n", "Done: OTULIN\n", "Done: OXSR1\n", "Done: P2RY1\n", "Done: P4HB\n", "Done: PA2G4\n", "Done: PABIR1\n", "Done: PACSIN1\n", "Done: PACSIN2\n", "Done: PAG1\n", "Done: PAGE4\n", "Done: PAK1\n", "Done: PAK4\n", "Done: PAK6\n", "Done: PARD3\n", "Done: PARD3B\n", "Done: PARK7\n", "Done: PARP1\n", "Done: PARP10\n", "Done: PARVA\n", "Done: PBK\n", "Done: PCGF2\n", "Done: PCNA\n", "Done: PCYT1A\n", "Done: PDCD4\n", "Done: PDCD6IP\n", "Done: PDCL\n", "Done: PDE3A\n", "Done: PDE3B\n", "Done: PDGFRA\n", "Done: PDGFRB\n", "Done: PDHA1\n", "Done: PDP1\n", "Done: PDPK1\n", "Done: PDZK1\n", "Done: PEAK1\n", "Done: PEBP1\n", "Done: PES1\n", "Done: PEX14\n", "Done: PEX5\n", "Done: PFKFB2\n", "Done: PFKP\n", "Done: PFN1\n", "Done: PGK1\n", "Done: PGR\n", "Done: PHB1\n", "Done: PHB2\n", "Done: PHF8\n", "Done: PICK1\n", "Done: PIDD1\n", "Done: PIK3C3\n", "Done: PIK3CG\n", "Done: PIK3R1\n", "Done: PIK3R2\n", "Done: PIN1\n", "Done: PIP5K1C\n", "Done: PITPNC1\n", "Done: PKM\n", "Done: PKMYT1\n", "Done: PKP1\n", "Done: PKP2\n", "Done: PKP3\n", "Done: PLCG1\n", "Done: PLEC\n", "Done: PLEKHG2\n", "Done: PLEKHG6\n", "Done: PLK1\n", "Done: PLN\n", "Done: PLSCR1\n", "Done: PLXNB1\n", "Done: PMAIP1\n", "Done: PML\n", "Done: POLE\n", "Done: POLL\n", "Done: POLR2A\n", "Done: POLR2M\n", "Done: POU5F1\n", "Done: PPARA\n", "Done: PPARD\n", "Done: PPIF\n", "Done: PPP1R12A\n", "Done: PPP1R12C\n", "Done: PPP1R13L\n", "Done: PPP1R16B\n", "Done: PPP2CA\n", "Done: PPP2R5C\n", "Done: PRC1\n", "Done: PRICKLE1\n", "Done: PRKACA\n", "Done: PRKAR1A\n", "Done: PRKCD\n", "Done: PRKCE\n", "Done: PRKD1\n", "Done: PRKD2\n", "Done: PRKDC\n", "Done: PRKN\n", "Done: PRKRA\n", "Done: PRLR\n", "Done: PRMT7\n", "Done: PROX1\n", "Done: PSEN1\n", "Done: PSEN2\n", "Done: PSMD1\n", "Done: PSMD2\n", "Done: PSME3\n", "Done: PTEN\n", "Done: PTGES3\n", "Done: PTK2\n", "Done: PTK2B\n", "Done: PTPN11\n", "Done: PTPN12\n", "Done: PTPN22\n", "Done: PTPN6\n", "Done: PTPRJ\n", "Done: PTS\n", "Done: PTTG1IP\n", "Done: PXN\n", "Done: Piwi\n", "Done: Pop-1\n", "Done: RAB11FIP5\n", "Done: RAB1A\n", "Done: RAB7A\n", "Done: RAB8A\n", "Done: RABEP1\n", "Done: RAC1\n", "Done: RACGAP1\n", "Done: RACK1\n", "Done: RAD51\n", "Done: RAD52\n", "Done: RAD9A\n", "Done: RAF1\n", "Done: RAG2\n", "Done: RALGAPA2\n", "Done: RAN\n", "Done: RANGAP1\n", "Done: RAP1A\n", "Done: RAP1B\n", "Done: RAP1GAP\n", "Done: RAP1GAP2\n", "Done: RAPGEF2\n", "Done: RARA\n", "Done: RB1\n", "Done: RBBP5\n", "Done: RBBP8\n", "Done: RBL1\n", "Done: RBL2\n", "Done: RBM25\n", "Done: RBM38\n", "Done: RBM4\n", "Done: RBM7\n", "Done: RC3H2\n", "Done: RCC1\n", "Done: RCHY1\n", "Done: RECQL4\n", "Done: RELA\n", "Done: RELB\n", "Done: REM1\n", "Done: REST\n", "Done: RET\n", "Done: RETREG1\n", "Done: RGS18\n", "Done: RGS5\n", "Done: RGS7\n", "Done: RHO\n", "Done: RHOA\n", "Done: RICTOR\n", "Done: RIMS1\n", "Done: RIN1\n", "Done: RIPK1\n", "Done: RIPK2\n", "Done: RIPK3\n", "Done: RMDN3\n", "Done: RND3\n", "Done: RNF187\n", "Done: RNMT\n", "Done: ROCK2\n", "Done: RORA\n", "Done: RPA1\n", "Done: RPS10\n", "Done: RPTOR\n", "Done: RRM1\n", "Done: RRM2\n", "Done: RRN3\n", "Done: RUNX1\n", "Done: RUNX3\n", "Done: RUVBL2\n", "Done: RXRA\n", "Done: S100A11\n", "Done: SAFB\n", "Done: SAMSN1\n", "Done: SASH1\n", "Done: SATB1\n", "Done: SCN1A\n", "Done: SCN5A\n", "Done: SDC1\n", "Done: SDC2\n", "Done: SDC4\n", "Done: SDCBP\n", "Done: SEC23A\n", "Done: SEC23B\n", "Done: SEC63\n", "Done: SECISBP2L\n", "Done: SELL\n", "Done: SEPTIN12\n", "Done: SEPTIN7\n", "Done: SERINC3\n", "Done: SF3B2\n", "Done: SFN\n", "Done: SFPQ\n", "Done: SGK3\n", "Done: SGO1\n", "Done: SGTA\n", "Done: SH2D1B\n", "Done: SH2D2A\n", "Done: SH3BP2\n", "Done: SH3BP4\n", "Done: SH3GL1\n", "Done: SH3GL2\n", "Done: SH3KBP1\n", "Done: SH3RF1\n", "Done: SHCBP1\n", "Done: SHOC2\n", "Done: SIAH1\n", "Done: SIGIRR\n", "Done: SIK3\n", "Done: SIRT1\n", "Done: SIRT2\n", "Done: SIRT7\n", "Done: SIT1\n", "Done: SKA3\n", "Done: SKAP1\n", "Done: SKP2\n", "Done: SLC2A1\n", "Done: SLC4A1\n", "Done: SLC9A1\n", "Done: SLC9A3R1\n", "Done: SLC9A3R2\n", "Done: SLD2\n", "Done: SLITRK1\n", "Done: SMAD1\n", "Done: SMAD2\n", "Done: SMAD3\n", "Done: SMAD4\n", "Done: SMAD7\n", "Done: SMARCA4\n", "Done: SMC1A\n", "Done: SMG9\n", "Done: SMN1\n", "Done: SMURF2\n", "Done: SNAI1\n", "Done: SNAI2\n", "Done: SNAP23\n", "Done: SNAP25\n", "Done: SNAP91\n", "Done: SNAPIN\n", "Done: SNCA\n", "Done: SNCAIP\n", "Done: SND1\n", "Done: SNW1\n", "Done: SNX27\n", "Done: SNX5\n", "Done: SNX8\n", "Done: SOCS1\n", "Done: SOCS3\n", "Done: SOD1\n", "Done: SORBS2\n", "Done: SOS1\n", "Done: SOX2\n", "Done: SOX9\n", "Done: SP1\n", "Done: SPHK1\n", "Done: SPI1\n", "Done: SPOP\n", "Done: SPRED1\n", "Done: SPRR2B\n", "Done: SPRY2\n", "Done: SPSB1\n", "Done: SQSTM1\n", "Done: SRC\n", "Done: SREBF1\n", "Done: SRPK2\n", "Done: SRY\n", "Done: SSH1\n", "Done: SSTR2\n", "Done: STAP2\n", "Done: STAR\n", "Done: STARD3\n", "Done: STAT1\n", "Done: STAT2\n", "Done: STAT3\n", "Done: STAT4\n", "Done: STAT6\n", "Done: STIL\n", "Done: STIM1\n", "Done: STING1\n", "Done: STK11\n", "Done: STK3\n", "Done: STK38\n", "Done: STK4\n", "Done: STMN1\n", "Done: STX17\n", "Done: STX1A\n", "Done: STXBP2\n", "Done: STYK1\n", "Done: SUFU\n", "Done: SULT4A1\n", "Done: SUZ12\n", "Done: SVIL\n", "Done: SWAP70\n", "Done: SYK\n", "Done: Slob\n", "Done: TACSTD2\n", "Done: TAGAP\n", "Done: TAGLN\n", "Done: TAGLN2\n", "Done: TAL1\n", "Done: TARBP2\n", "Done: TARDBP\n", "Done: TBC1D1\n", "Done: TBC1D4\n", "Done: TBK1\n", "Done: TBL1X\n", "Done: TCF21\n", "Done: TCF3\n", "Done: TCOF1\n", "Done: TDP1\n", "Done: TELO2\n", "Done: TERF1\n", "Done: TERF2\n", "Done: TERT\n", "Done: TET2\n", "Done: TFEB\n", "Done: TGFB1I1\n", "Done: TGFBR1\n", "Done: TGFBR2\n", "Done: TGFBR3\n", "Done: TGM2\n", "Done: TH\n", "Done: THRB\n", "Done: TIAM1\n", "Done: TICAM1\n", "Done: TIGIT\n", "Done: TIMELESS\n", "Done: TIMP2\n", "Done: TJP1\n", "Done: TK1\n", "Done: TNFAIP1\n", "Done: TNFAIP8L2\n", "Done: TNFRSF1A\n", "Done: TNK2\n", "Done: TNNI3\n", "Done: TOB2\n", "Done: TOM1L1\n", "Done: TOP1\n", "Done: TOP2A\n", "Done: TOPBP1\n", "Done: TOPORS\n", "Done: TP53\n", "Done: TP53BP1\n", "Done: TP73\n", "Done: TPH2\n", "Done: TPK1\n", "Done: TPS5\n", "Done: TPT1\n", "Done: TRADD\n", "Done: TRAF2\n", "Done: TRAF3\n", "Done: TRAPPC6A\n", "Done: TRIM11\n", "Done: TRIM14\n", "Done: TRIM21\n", "Done: TRIM24\n", "Done: TRIM28\n", "Done: TRIM29\n", "Done: TRIM32\n", "Done: TRIM33\n", "Done: TRIM59\n", "Done: TRIP10\n", "Done: TRPC4\n", "Done: TRPV4\n", "Done: TSC1\n", "Done: TSC2\n", "Done: TTI1\n", "Done: TTK\n", "Done: TUBA1A\n", "Done: UBE2I\n", "Done: UBE2J1\n", "Done: UBTF\n", "Done: UFD1\n", "Done: UFL1\n", "Done: UHRF1\n", "Done: ULK1\n", "Done: ULK2\n", "Done: UNG\n", "Done: UPF1\n", "Done: URI1\n", "Done: USP13\n", "Done: USP15\n", "Done: USP16\n", "Done: USP20\n", "Done: USP21\n", "Done: USP4\n", "Done: USP8\n", "Done: UTRN\n", "Done: UVRAG\n", "Done: VASP\n", "Done: VAV1\n", "Done: VCP\n", "Done: VCPIP1\n", "Done: VDR\n", "Done: VGLL1\n", "Done: VHL\n", "Done: VIM\n", "Done: VRK3\n", "Done: WAS\n", "Done: WASF1\n", "Done: WDHD1\n", "Done: WDR62\n", "Done: WEE1\n", "Done: WIPF1\n", "Done: WNK1\n", "Done: WRAP53\n", "Done: WRN\n", "Done: WWOX\n", "Done: WWP2\n", "Done: WWTR1\n", "Done: XIAP\n", "Done: XPA\n", "Done: XRCC1\n", "Done: XRCC4\n", "Done: XRCC6\n", "Done: YAP1\n", "Done: YWHAH\n", "Done: YWHAZ\n", "Done: Yki\n", "Done: ZAP70\n", "Done: ZBTB7A\n", "Done: ZEB2\n", "Done: ZFP36L1\n", "Done: ZMYM2\n", "Done: ZNF281\n", "Done: ZNF282\n", "Done: ZNF76\n", "Done: ZNRF2\n", "Done: ZWINT\n", "Done: ZYX\n" ] } ], "source": [ "CSV_PATH = \"../data/ptmint_dataset.csv\"\n", "\n", "df = pd.read_csv(CSV_PATH)\n", "genes = sorted(set(df[\"Gene\"].dropna().astype(str)))\n", "\n", "header = [\n", "\"Organism\",\"Gene\",\"Uniprot\",\"PTM\",\"Site\",\"AA\",\"Int_uniprot\",\"Int_gene\",\n", "\"Effect\",\"Method\",\"Disease\",\"Co_localized\",\"PMID\",\"Complex\",\"Origin\",\n", "\"Confidence\",\"PDBRES\",\"Score\",\"Interface\",\"Domain\"\n", "]\n", "\n", "os.makedirs(\"../data/protein_features\", exist_ok=True)\n", "\n", "with open(\"../data/ptmint_iufeatures.txt\", \"w\") as out:\n", "\n", " out.write(\"\\t\".join(header) + \"\\n\")\n", "\n", " for gene in genes:\n", "\n", " # ---- scrape interaction table ----\n", " url = f\"https://ptmint.sjtu.edu.cn/Search/Phos/{gene}\"\n", " r = requests.get(url)\n", "\n", " soup = BeautifulSoup(r.text, \"html.parser\")\n", " table = soup.find(\"table\", {\"id\": \"data\"})\n", "\n", " if table is not None:\n", " for tr in table.find_all(\"tr\")[1:]:\n", " cols = [td.get_text(strip=True) for td in tr.find_all(\"td\")]\n", " out.write(\"\\t\".join(cols) + \"\\n\")\n", "\n", " # ---- download protein feature csv ----\n", " feat_url = f\"https://ptmint.sjtu.edu.cn/data/{gene}_protein_features.csv\"\n", " feat_file = f\"../data/protein_features/{gene}_protein_features.csv\"\n", "\n", " rf = requests.get(feat_url)\n", " if rf.status_code == 200:\n", " with open(feat_file, \"wb\") as f:\n", " f.write(rf.content)\n", "\n", " print(\"Done:\", gene)\n", "\n", " time.sleep(0.3)\n", "\n", "input_file = \"../data/ptmint_iufeatures.txt\"\n", "output_file = \"../data/ptmint_iufeatures.csv\"\n", "df = pd.read_csv(input_file, sep=\"\\t\")\n", "df.to_csv(output_file, index=False)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 3. Get additional information (sequence strings, unify with interface data)" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import os\n", "import pandas as pd\n", "from Bio.PDB import PDBParser, PPBuilder\n", "\n", "pd.set_option('display.max_columns', None)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Interacting chain names and sequences" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "PDB_DIR = \"../data/ProteinStructures/Complexes\"\n", "STRUCT_DF = \"../data/ptmint_iufeatures.csv\"\n", "parser = PDBParser(QUIET=True)\n", "ppb = PPBuilder()\n", "\n", "df = pd.read_csv(\"/nfs/turbo/umms-ajitj/PTMint/data/ptmint_iufeatures.csv\")\n", "\n", "def get_chain_sequence_from_structure(structure, chain_id):\n", " model = structure[0]\n", " if chain_id not in model:\n", " return \"\"\n", " chain = model[chain_id]\n", " peptides = ppb.build_peptides(chain)\n", " if not peptides:\n", " return \"\"\n", " return \"\".join(str(pp.get_sequence()) for pp in peptides)\n", "\n", "def get_two_chain_ids(pdb_path):\n", " \"\"\"Return the two chain IDs in model 0. If not exactly 2, return what exists.\"\"\"\n", " structure = parser.get_structure(\"complex\", pdb_path)\n", " model = structure[0]\n", " chain_ids = [c.id for c in model.get_chains()]\n", " return structure, chain_ids\n", "\n", "def extract_two_chain_seqs(pdb_path):\n", " \"\"\"\n", " Returns:\n", " (chain1_id, seq1, chain2_id, seq2)\n", " Assumes exactly 2 chains, but doesn't crash if not.\n", " \"\"\"\n", " structure, chain_ids = get_two_chain_ids(pdb_path)\n", "\n", " if len(chain_ids) < 2:\n", " c1 = chain_ids[0] if len(chain_ids) == 1 else \"\"\n", " s1 = get_chain_sequence_from_structure(structure, c1) if c1 else \"\"\n", " return c1, s1, \"\", \"\"\n", "\n", " if len(chain_ids) > 2:\n", " # PTMint says it should be exactly 2; fail loudly so you notice bad files.\n", " raise ValueError(f\"{pdb_path} has {len(chain_ids)} chains: {chain_ids} (expected exactly 2)\")\n", "\n", " c1, c2 = chain_ids[0], chain_ids[1]\n", " s1 = get_chain_sequence_from_structure(structure, c1)\n", " s2 = get_chain_sequence_from_structure(structure, c2)\n", " return c1, s1, c2, s2\n", "\n", "def add_interactor_sequences(df):\n", " df = df.copy()\n", " df[\"pdb_path\"] = df[\"Complex\"].astype(str).str.replace(\".pdb\", \"\", regex=False) \\\n", " .apply(lambda x: os.path.join(PDB_DIR, f\"{x}.pdb\"))\n", "\n", " out = df[\"pdb_path\"].apply(extract_two_chain_seqs)\n", "\n", " df[\"Interactor_chain_1\"] = out.apply(lambda t: t[0])\n", " df[\"Interactor_1_seq\"] = out.apply(lambda t: t[1])\n", " df[\"Interactor_chain_2\"] = out.apply(lambda t: t[2])\n", " df[\"Interactor_2_seq\"] = out.apply(lambda t: t[3])\n", "\n", " return df\n", "\n", "df = add_interactor_sequences(df)\n", "df.drop(columns=[\"pdb_path\"], inplace=True)\n", "\n", "output_file = \"../data/ptmint_with_seqs.csv\"\n", "df.to_csv(output_file, index=False)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Interface residue numbers and names" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "output_file = \"../data/ptmint_with_seqs.csv\"\n", "df = pd.read_csv(output_file)\n", "\n", "# 1) Read interface residues\n", "iface = pd.read_csv(\n", " \"../data/ProteinStructures/complex_interface.csv\"\n", ")\n", "\n", "aa3_to_aa1 = {\n", " \"ALA\":\"A\",\"ARG\":\"R\",\"ASN\":\"N\",\"ASP\":\"D\",\"CYS\":\"C\",\n", " \"GLN\":\"Q\",\"GLU\":\"E\",\"GLY\":\"G\",\"HIS\":\"H\",\"ILE\":\"I\",\n", " \"LEU\":\"L\",\"LYS\":\"K\",\"MET\":\"M\",\"PHE\":\"F\",\"PRO\":\"P\",\n", " \"SER\":\"S\",\"THR\":\"T\",\"TRP\":\"W\",\"TYR\":\"Y\",\"VAL\":\"V\"\n", "}\n", "\n", "iface[\"AA1\"] = iface[\"AA\"].map(aa3_to_aa1).fillna(\"X\")\n", "\n", "# ------------------------------------------------\n", "# 2) interface_sites_num → {chain: \"site1,site2,...\"}\n", "# ------------------------------------------------\n", "\n", "sites_agg = (\n", " iface.groupby([\"Complex\", \"Chain\"])[\"Site\"]\n", " .apply(lambda s: \",\".join(map(str, s.tolist())))\n", " .reset_index(name=\"sites\")\n", ")\n", "\n", "sites_dict = (\n", " sites_agg.groupby(\"Complex\")\n", " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"sites\"])))\n", " .to_dict()\n", ")\n", "\n", "df[\"interface_sites_num\"] = df[\"Complex\"].map(sites_dict).apply(\n", " lambda x: x if isinstance(x, dict) else {}\n", ")\n", "\n", "# ------------------------------------------------\n", "# 3) interface_sequence_dict → {chain: \"A,S,T,...\"}\n", "# ------------------------------------------------\n", "\n", "seq_agg = (\n", " iface.groupby([\"Complex\", \"Chain\"])[\"AA1\"]\n", " .apply(lambda s: \",\".join(s.tolist()))\n", " .reset_index(name=\"seqs\")\n", ")\n", "\n", "seq_dict = (\n", " seq_agg.groupby(\"Complex\")\n", " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"seqs\"])))\n", " .to_dict()\n", ")\n", "\n", "df[\"interface_sequence_dict\"] = df[\"Complex\"].map(seq_dict).apply(\n", " lambda x: x if isinstance(x, dict) else {}\n", ")\n", "\n", "df_original = pd.read_csv(\"../data/ptmint_dataset.csv\")\n", "df.to_csv(\"../intermediate/ptmint_interm.csv\", index=False)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 4. Extract sequence information from complexes PDBs" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "import os\n", "from pathlib import Path\n", "from Bio.PDB import PDBParser, PPBuilder\n", "import time\n", "import requests\n", "import pandas as pd" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wrote 2960 rows -> ../data/complex_chain_seqs.csv\n" ] } ], "source": [ "PDB_DIR = Path(\"../data/ProteinStructures/Complexes\")\n", "OUT_CSV = Path(\"../data/complex_chain_seqs.csv\")\n", "\n", "parser = PDBParser(QUIET=True)\n", "ppb = PPBuilder()\n", "\n", "def get_chain_sequence_from_structure(structure, chain_id: str) -> str:\n", " model = structure[0]\n", " if chain_id not in model:\n", " return \"\"\n", " chain = model[chain_id]\n", " peptides = ppb.build_peptides(chain)\n", " if not peptides:\n", " return \"\"\n", " # Concatenate peptide fragments (handles chain breaks)\n", " return \"\".join(str(pp.get_sequence()) for pp in peptides)\n", "\n", "def extract_two_chain_seqs(pdb_path: Path):\n", " \"\"\"\n", " Returns (c1, s1, c2, s2).\n", " Raises if more than 2 chains (so you notice unexpected files).\n", " \"\"\"\n", " structure = parser.get_structure(pdb_path.stem, str(pdb_path))\n", " model = structure[0]\n", " chain_ids = [c.id for c in model.get_chains()]\n", "\n", " if len(chain_ids) == 0:\n", " return \"\", \"\", \"\", \"\"\n", " if len(chain_ids) == 1:\n", " c1 = chain_ids[0]\n", " s1 = get_chain_sequence_from_structure(structure, c1)\n", " return c1, s1, \"\", \"\"\n", " if len(chain_ids) > 2:\n", " raise ValueError(f\"{pdb_path} has {len(chain_ids)} chains: {chain_ids} (expected exactly 2)\")\n", "\n", " c1, c2 = chain_ids[0], chain_ids[1]\n", " s1 = get_chain_sequence_from_structure(structure, c1)\n", " s2 = get_chain_sequence_from_structure(structure, c2)\n", " return c1, s1, c2, s2\n", "\n", "rows = []\n", "errors = []\n", "\n", "for pdb_path in sorted(PDB_DIR.glob(\"*.pdb\")):\n", " complex_name = pdb_path.name # keep .pdb in Complex; change to pdb_path.stem if you want no extension\n", " try:\n", " c1, s1, c2, s2 = extract_two_chain_seqs(pdb_path)\n", " rows.append({\n", " \"Complex\": complex_name,\n", " \"Interactor_chain_1\": c1,\n", " \"Interactor_1_seq\": s1,\n", " \"Interactor_chain_2\": c2,\n", " \"Interactor_2_seq\": s2,\n", " })\n", " except Exception as e:\n", " errors.append((pdb_path.name, str(e)))\n", "\n", "df_out = pd.DataFrame(rows, columns=[\n", " \"Complex\",\n", " \"Interactor_chain_1\", \"Interactor_1_seq\",\n", " \"Interactor_chain_2\", \"Interactor_2_seq\",\n", "])\n", "\n", "OUT_CSV.parent.mkdir(parents=True, exist_ok=True)\n", "df_out.to_csv(OUT_CSV, index=False)\n", "\n", "print(f\"Wrote {len(df_out)} rows -> {OUT_CSV}\")\n", "if errors:\n", " print(\"\\nFiles with errors:\")\n", " for fn, msg in errors:\n", " print(f\" {fn}: {msg}\")" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wrote: ../intermediate/ptmint_merged_with_uniprot_seqs.csv (rows=5156)\n" ] } ], "source": [ "df_original = pd.read_csv(\"../data/ptmint_dataset.csv\")\n", "df_original = df_original.rename(columns={\"Sequence window(-5,+5)\": \"SequenceWindow\"})\n", "df_new = pd.read_csv(\"../intermediate/ptmint_interm.csv\").drop_duplicates()\n", "\n", "merge_keys = [\n", " 'Organism', 'Gene', 'Uniprot', 'PTM', 'Site', 'AA',\n", " 'Int_uniprot', 'Int_gene', 'Effect', 'Method', 'Disease', 'PMID'\n", "]\n", "\n", "df2 = df_original.merge(\n", " df_new,\n", " on=merge_keys,\n", " how='left',\n", ")\n", "\n", "df2.to_csv(\"../intermediate/ptmint_merged.csv\", index=False)\n", "\n", "\n", "INPUT_CSV = \"../intermediate/ptmint_merged.csv\"\n", "OUTPUT_CSV = \"../intermediate/ptmint_merged_with_uniprot_seqs.csv\"\n", "\n", "UNIPROT_FASTA_URL = \"https://rest.uniprot.org/uniprotkb/{}.fasta\"\n", "\n", "SLEEP_BETWEEN_REbQUESTS_SEC = 0.05\n", "TIMEOUT_SEC = 30\n", "\n", "session = requests.Session()\n", "\n", "def fasta_to_sequence(fasta_text: str) -> str:\n", " \"\"\"Convert FASTA text into a single continuous AA sequence string.\"\"\"\n", " if not fasta_text:\n", " return \"\"\n", " lines = [ln.strip() for ln in fasta_text.splitlines() if ln.strip()]\n", " if not lines:\n", " return \"\"\n", " # drop header lines starting with '>'\n", " seq_lines = [ln for ln in lines if not ln.startswith(\">\")]\n", " return \"\".join(seq_lines).replace(\" \", \"\")\n", "\n", "def fetch_uniprot_sequence(uniprot_id: str) -> str:\n", " \"\"\"Download FASTA from UniProt and return the AA sequence; return '' on failure.\"\"\"\n", " if uniprot_id is None:\n", " return \"\"\n", " uniprot_id = str(uniprot_id).strip()\n", " if uniprot_id == \"\" or uniprot_id.lower() in {\"nan\", \"none\"}:\n", " return \"\"\n", "\n", " url = UNIPROT_FASTA_URL.format(uniprot_id)\n", "\n", " try:\n", " r = session.get(url, timeout=TIMEOUT_SEC)\n", " if r.status_code != 200:\n", " return \"\"\n", " return fasta_to_sequence(r.text)\n", " except requests.RequestException:\n", " return \"\"\n", "\n", "def add_sequences(df: pd.DataFrame) -> pd.DataFrame:\n", " df = df.copy()\n", "\n", " # Cache to avoid repeated downloads\n", " cache = {}\n", "\n", " def cached_get(acc):\n", " acc_str = \"\" if pd.isna(acc) else str(acc).strip()\n", " if acc_str == \"\" or acc_str.lower() in {\"nan\", \"none\"}:\n", " return \"\"\n", " if acc_str in cache:\n", " return cache[acc_str]\n", " seq = fetch_uniprot_sequence(acc_str)\n", " cache[acc_str] = seq\n", " time.sleep(SLEEP_BETWEEN_REQUESTS_SEC)\n", " return seq\n", "\n", " # Create / overwrite columns\n", " df[\"Gene_sequence\"] = df[\"Uniprot\"].apply(cached_get)\n", " df[\"Int_gene_sequence\"] = df[\"Int_uniprot\"].apply(cached_get)\n", "\n", " return df\n", "\n", "df = pd.read_csv(INPUT_CSV)\n", "\n", "df2 = add_sequences(df)\n", "\n", "df2.to_csv(OUTPUT_CSV, index=False)\n", "print(f\"Wrote: {OUTPUT_CSV} (rows={len(df2)})\")" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Exact matches: 4376 / 5156\n" ] } ], "source": [ "import pandas as pd\n", "\n", "df_uniprot = pd.read_csv(\"../intermediate/ptmint_merged_with_uniprot_seqs.csv\")\n", "df_complex = pd.read_csv(\"../data/complex_chain_seqs.csv\")\n", "\n", "# --- build a \"normalized\" key so chain order doesn't matter ---\n", "def make_key(a, b):\n", " # treat (a,b) same as (b,a)\n", " return (a, b) if a <= b else (b, a)\n", "\n", "df_u = df_uniprot.copy()\n", "df_c = df_complex.copy()\n", "\n", "df_u[\"seqA\"] = df_u[\"Gene_sequence\"].fillna(\"\")\n", "df_u[\"seqB\"] = df_u[\"Int_gene_sequence\"].fillna(\"\")\n", "df_c[\"seq1\"] = df_c[\"Interactor_1_seq\"].fillna(\"\")\n", "df_c[\"seq2\"] = df_c[\"Interactor_2_seq\"].fillna(\"\")\n", "\n", "# optional: strip whitespace/newlines, common in fasta-like strings\n", "for col in [\"seqA\",\"seqB\"]:\n", " df_u[col] = df_u[col].str.replace(r\"\\s+\", \"\", regex=True)\n", "for col in [\"seq1\",\"seq2\"]:\n", " df_c[col] = df_c[col].str.replace(r\"\\s+\", \"\", regex=True)\n", "\n", "df_u[[\"k1\",\"k2\"]] = df_u.apply(lambda r: pd.Series(make_key(r[\"seqA\"], r[\"seqB\"])), axis=1)\n", "df_c[[\"k1\",\"k2\"]] = df_c.apply(lambda r: pd.Series(make_key(r[\"seq1\"], r[\"seq2\"])), axis=1)\n", "\n", "# If df_complex has duplicates for the same (k1,k2), decide how to handle:\n", "# e.g., keep first (or you can keep all and do one-to-many)\n", "df_c_dedup = df_c.drop_duplicates(subset=[\"k1\",\"k2\"], keep=\"first\")\n", "\n", "df_exact = df_u.merge(\n", " df_c_dedup[[\"Complex\",\"Interactor_chain_1\",\"Interactor_1_seq\",\"Interactor_chain_2\",\"Interactor_2_seq\",\"k1\",\"k2\"]],\n", " on=[\"k1\",\"k2\"],\n", " how=\"left\",\n", " suffixes=(\"\", \"_from_complex\")\n", ")\n", "\n", "exact_hit_mask = df_exact[\"Complex_from_complex\"].notna()\n", "print(\"Exact matches:\", exact_hit_mask.sum(), \" / \", len(df_exact))" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffect...seqAseqBk1k2Complex_from_complexInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexComplex_from_complex_clean
112HumanAKT1S1Q96B36Phos183SQQYAKsLPVSVQ8N122RPTORInhibit...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132.pdbAMASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...BMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132
113HumanAKT1S1Q96B36Phos183SQQYAKsLPVSVQ8N122RPTORInhibit...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132.pdbAMASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...BMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132
250HumanATG4BQ9Y4P1Phos316SAELDPsIAVGFQ9GZQ8MAP1LC3BInhibit...MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV...MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV...MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV...MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV...Complex3327.pdbAMPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV...BMDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV...Complex3327
667HumanCDH1P12830Phos790TNDVAPtLMSVPP35222CTNNB1Inhibit...MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL...Complex1370_1.pdbAMGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL...BMATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...Complex1370_1
671HumanCDH5P33151Phos731YDTLHIyGYEGSP35222CTNNB1Inhibit...MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK...Complex1357_1.pdbAMQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK...BMATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...Complex1357_1
..................................................................
1749HumanERBB4Q15303Phos1202YKAEDEyVNEPLP43405SYKEnhance...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...Complex2614_1.pdbAMKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...BMASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...Complex2614_1
1751HumanERBB4Q15303Phos1202YKAEDEyVNEPLP43405SYKEnhance...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...Complex2614_1.pdbAMKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...BMASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...Complex2614_1
1752HumanERBB4Q15303Phos1202YKAEDEyVNEPLP43405SYKEnhance...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...Complex2614_1.pdbAMKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...BMASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...Complex2614_1
1791HumanEZH2Q15910Phos311TYKRKNtETALDQ15022SUZ12Inhibit...MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR...MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC...MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC...MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR...Complex2565.pdbAMAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC...BMGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR...Complex2565
4523HumanSTK11Q15831Phos307SQIRQHsWFRKKQ7RTN6STRADAEnhance...MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI...MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS...MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI...MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS...Complex2687.pdbAMEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI...BMSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS...Complex2687
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396 rows × 41 columns

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" ], "text/plain": [ " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", "112 Human AKT1S1 Q96B36 Phos 183 S QQYAKsLPVSV Q8N122 \n", "113 Human AKT1S1 Q96B36 Phos 183 S QQYAKsLPVSV Q8N122 \n", "250 Human ATG4B Q9Y4P1 Phos 316 S AELDPsIAVGF Q9GZQ8 \n", "667 Human CDH1 P12830 Phos 790 T NDVAPtLMSVP P35222 \n", "671 Human CDH5 P33151 Phos 731 Y DTLHIyGYEGS P35222 \n", "... ... ... ... ... ... .. ... ... \n", "1749 Human ERBB4 Q15303 Phos 1202 Y KAEDEyVNEPL P43405 \n", "1751 Human ERBB4 Q15303 Phos 1202 Y KAEDEyVNEPL P43405 \n", "1752 Human ERBB4 Q15303 Phos 1202 Y KAEDEyVNEPL P43405 \n", "1791 Human EZH2 Q15910 Phos 311 T YKRKNtETALD Q15022 \n", "4523 Human STK11 Q15831 Phos 307 S QIRQHsWFRKK Q7RTN6 \n", "\n", " Int_gene Effect ... \\\n", "112 RPTOR Inhibit ... \n", "113 RPTOR Inhibit ... \n", "250 MAP1LC3B Inhibit ... \n", "667 CTNNB1 Inhibit ... \n", "671 CTNNB1 Inhibit ... \n", "... ... ... ... \n", "1749 SYK Enhance ... \n", "1751 SYK Enhance ... \n", "1752 SYK Enhance ... \n", "1791 SUZ12 Inhibit ... \n", "4523 STRADA Enhance ... \n", "\n", " seqA \\\n", "112 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", "113 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", "250 MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV... \n", "667 MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL... \n", "671 MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK... \n", "... ... \n", "1749 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", "1751 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", "1752 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", "1791 MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR... \n", "4523 MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI... \n", "\n", " seqB \\\n", "112 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", "113 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", "250 MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV... \n", "667 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", "671 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", "... ... \n", "1749 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1751 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1752 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1791 MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC... \n", "4523 MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS... \n", "\n", " k1 \\\n", "112 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", "113 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", "250 MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV... \n", "667 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", "671 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", "... ... \n", "1749 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1751 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1752 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1791 MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC... \n", "4523 MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI... \n", "\n", " k2 Complex_from_complex \\\n", "112 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... Complex3132.pdb \n", "113 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... Complex3132.pdb \n", "250 MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV... Complex3327.pdb \n", "667 MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL... Complex1370_1.pdb \n", "671 MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK... Complex1357_1.pdb \n", "... ... ... \n", "1749 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... Complex2614_1.pdb \n", "1751 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... Complex2614_1.pdb \n", "1752 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... Complex2614_1.pdb \n", "1791 MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR... Complex2565.pdb \n", "4523 MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS... Complex2687.pdb \n", "\n", " Interactor_chain_1_from_complex \\\n", "112 A \n", "113 A \n", "250 A \n", "667 A \n", "671 A \n", "... ... \n", "1749 A \n", "1751 A \n", "1752 A \n", "1791 A \n", "4523 A \n", "\n", " Interactor_1_seq_from_complex \\\n", "112 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", "113 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", "250 MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV... \n", "667 MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL... \n", "671 MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK... \n", "... ... \n", "1749 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", "1751 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", "1752 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", "1791 MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC... \n", "4523 MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI... \n", "\n", " Interactor_chain_2_from_complex \\\n", "112 B \n", "113 B \n", "250 B \n", "667 B \n", "671 B \n", "... ... \n", "1749 B \n", "1751 B \n", "1752 B \n", "1791 B \n", "4523 B \n", "\n", " Interactor_2_seq_from_complex \\\n", "112 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", "113 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", "250 MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV... \n", "667 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", "671 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", "... ... \n", "1749 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1751 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1752 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", "1791 MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR... \n", "4523 MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS... \n", "\n", " Complex_from_complex_clean \n", "112 Complex3132 \n", "113 Complex3132 \n", "250 Complex3327 \n", "667 Complex1370_1 \n", "671 Complex1357_1 \n", "... ... \n", "1749 Complex2614_1 \n", "1751 Complex2614_1 \n", "1752 Complex2614_1 \n", "1791 Complex2565 \n", "4523 Complex2687 \n", "\n", "[396 rows x 41 columns]" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Check for differences between complex ID from website and obtained through alignment\n", "df_exact[\"Complex_from_complex_clean\"] = (\n", " df_exact[\"Complex_from_complex\"]\n", " .str.replace(\".pdb\", \"\", regex=False)\n", ")\n", "\n", "df_exact[\n", " df_exact[\"Complex\"].notna() &\n", " df_exact[\"Complex_from_complex_clean\"].notna() &\n", " (df_exact[\"Complex\"] != \"\") &\n", " (df_exact[\"Complex_from_complex_clean\"] != \"\") &\n", " (df_exact[\"Complex\"] != df_exact[\"Complex_from_complex_clean\"])\n", "]" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Rows where Complex_from_complex exists but Complex is missing: 185\n" ] } ], "source": [ "rows = df_exact[\n", " df_exact[\"Complex\"].notna() &\n", " df_exact[\"Complex_from_complex\"].isna()\n", "]\n", "\n", "print(\"Rows where Complex_from_complex exists but Complex is missing:\", len(rows))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "df_exact populate the column Complex with Complex_from_complex_clean when Complex is empty or na and then drop cols seqA, seqB, k1, k2, Complex_from_complex_clean" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "# Populate in df_exact the column Complex with Complex_from_complex_clean when Complex is empty or na\n", "\n", "df_exact[\"Complex\"] = df_exact[\"Complex\"].replace(\"\", pd.NA)\n", "df_exact[\"Complex_from_complex_clean\"] = df_exact[\"Complex_from_complex_clean\"].replace(\"\", pd.NA)\n", "df_exact[\"Complex\"] = df_exact[\"Complex\"].combine_first(df_exact[\"Complex_from_complex_clean\"])\n", "# # Drop helper columns\n", "df_exact = df_exact.drop(columns=[\"seqA\", \"seqB\", \"k1\", \"k2\", 'Complex_from_complex', 'Interactor_chain_1','Interactor_1_seq',\t'Interactor_chain_2',\t'Interactor_2_seq'])\n", "mask = df_exact[\"Complex_from_complex_clean\"].fillna(\"\") != df_exact[\"Complex\"].fillna(\"\")\n", "\n", "df_exact[\"Alternative_Complex\"] = None\n", "df_exact.loc[mask, \"Alternative_Complex\"] = df_exact.loc[mask, \"Complex_from_complex_clean\"]\n", "df_exact = df_exact.drop(columns=[\"Complex_from_complex_clean\"])" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "df_exact[\"hf_complex_path\"] = \"../data/ProteinStructures/Complexes/\" + df_exact[\"Complex\"].astype(str) + \".pdb\"\n" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "df = df_exact.copy()\n", "\n", "# 1) Read interface residues\n", "iface = pd.read_csv(\n", " \"../data/ProteinStructures/complex_interface.csv\"\n", ")\n", "\n", "aa3_to_aa1 = {\n", " \"ALA\":\"A\",\"ARG\":\"R\",\"ASN\":\"N\",\"ASP\":\"D\",\"CYS\":\"C\",\n", " \"GLN\":\"Q\",\"GLU\":\"E\",\"GLY\":\"G\",\"HIS\":\"H\",\"ILE\":\"I\",\n", " \"LEU\":\"L\",\"LYS\":\"K\",\"MET\":\"M\",\"PHE\":\"F\",\"PRO\":\"P\",\n", " \"SER\":\"S\",\"THR\":\"T\",\"TRP\":\"W\",\"TYR\":\"Y\",\"VAL\":\"V\"\n", "}\n", "\n", "iface[\"AA1\"] = iface[\"AA\"].map(aa3_to_aa1).fillna(\"X\")\n", "\n", "# ------------------------------------------------\n", "# 2) interface_sites_num → {chain: \"site1,site2,...\"}\n", "# ------------------------------------------------\n", "\n", "sites_agg = (\n", " iface.groupby([\"Complex\", \"Chain\"])[\"Site\"]\n", " .apply(lambda s: \",\".join(map(str, s.tolist())))\n", " .reset_index(name=\"sites\")\n", ")\n", "\n", "sites_dict = (\n", " sites_agg.groupby(\"Complex\")\n", " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"sites\"])))\n", " .to_dict()\n", ")\n", "\n", "df[\"interface_sites_num\"] = df[\"Complex\"].map(sites_dict).apply(\n", " lambda x: x if isinstance(x, dict) else {}\n", ")\n", "\n", "# ------------------------------------------------\n", "# 3) interface_sequence_dict → {chain: \"A,S,T,...\"}\n", "# ------------------------------------------------\n", "\n", "seq_agg = (\n", " iface.groupby([\"Complex\", \"Chain\"])[\"AA1\"]\n", " .apply(lambda s: \",\".join(s.tolist()))\n", " .reset_index(name=\"seqs\")\n", ")\n", "\n", "seq_dict = (\n", " seq_agg.groupby(\"Complex\")\n", " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"seqs\"])))\n", " .to_dict()\n", ")\n", "\n", "df[\"interface_sequence_dict\"] = df[\"Complex\"].map(seq_dict).apply(\n", " lambda x: x if isinstance(x, dict) else {}\n", ")\n", "\n", "# normalize capitalization\n", "df[\"Effect\"] = df[\"Effect\"].str.lower().str.capitalize()\n", "# convert Induce -> Enhance\n", "df[\"Effect\"] = df[\"Effect\"].replace(\"Induce\", \"Enhance\")" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Rows with Complex: 4561\n", "Rows without Complex: 595\n" ] } ], "source": [ "complex_col = df_exact[\"Complex\"].replace(\"\", pd.NA)\n", "\n", "num_with_complex = complex_col.notna().sum()\n", "num_without_complex = complex_col.isna().sum()\n", "\n", "print(\"Rows with Complex:\", num_with_complex)\n", "print(\"Rows without Complex:\", num_without_complex)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 5. Filling missing information on whether the phosphorylation site is in the interface" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Rows with Complex: 4561\n", "Rows lacking Complex: 595\n", "Rows where interface missing: 3015\n" ] } ], "source": [ "has_complex = df[\"Complex\"].notna() & (df[\"Complex\"].astype(str).str.strip() != \"\")\n", "print(\"Rows with Complex:\", has_complex.sum())\n", "print(\"Rows lacking Complex:\", (~has_complex).sum())\n", "\n", "df_with_complex = df[has_complex].copy()\n", "\n", "interface_missing = (\n", " df_with_complex[\"Interface\"].isna()\n", " | df_with_complex[\"Interface\"].eq(\"\")\n", ")\n", "\n", "print(\"Rows where interface missing:\", interface_missing.sum())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "pd.set_option('display.max_columns', None)\n" ] }, { "cell_type": "code", "execution_count": 39, "metadata": {}, "outputs": [], "source": [ "df_prev=df.copy()" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffectMethodDiseaseCo-localizedPMIDCo_localizedComplexOriginConfidencePDBRESScoreInterfaceDomaininterface_sites_numinterface_sequence_dicthf_complex_pathGene_sequenceInt_gene_sequenceInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexAlternative_Complex
0HumanAANATQ16613Phos31TCQRRHtLPASEP63104YWHAZEnhanceMolecular dynamics simulation(MD)NaNNaN28387381NaNComplex2735PyMOLMediumA31:THR0.50TrueNaN{'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,...{'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E...../data/ProteinStructures/Complexes/Complex273...MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...AMSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...BMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...None
1HumanAATFQ9NY61Phos366TVYRNRtLQKWHP19105MYL12AInhibitPeptide pull-downEndometrial cancerNaN22909821NaNComplex3475ZDOCKLowA366:THR0.50FalseAATF-Che1{'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,...{'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D...../data/ProteinStructures/Complexes/Complex347...MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...AMAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...BMSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...None
2HumanABCG2Q9UNQ0Phos362TKKKKItVFKEIQ9UNQ0ABCG2EnhanceCo-IPProstate cancerPlasma membrane18056989Plasma membraneComplex3607PyMOLMediumA362:THR0.50FalseNaN{'A': '44,46,48,53,56,63,81,82,83,88,97,126,12...{'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q...../data/ProteinStructures/Complexes/Complex360...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...AMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...BMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...None
3HumanABI1Q8IZP0Phos213YTVPNDyMTSPAP27986PIK3R1EnhanceAffinity capture binding assayNaNNaN20598684NaNComplex2954ZDOCKLowB213:TYR0.50FalseNaN{'A': '1,363,364,365,620,621,622,625,626,627,6...{'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q...../data/ProteinStructures/Complexes/Complex295...MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...AMSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...BMAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...None
4HumanABI3Q9P2A4Phos342SVTRRYsDGWCEQ7L576CYFIP1InhibitCo-IPThyroid cancerNaN28978070NaNComplex3517ZDOCKLowB342:SER0.75FalseSH3_9{'A': '781,782,785,788,831,832,833,834,835,836...{'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F...../data/ProteinStructures/Complexes/Complex351...MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...AMAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...BMAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...None
...................................................................................................
5151S. pombeKlp9Q1MTQ7Phos605SKKKVVsPIKPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...None
5152S. pombeKlp9Q1MTQ7Phos611SPIKPLsPSRRPQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...None
5153S. pombeKlp9Q1MTQ7Phos613SKPLSPsRRPPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...None
5154S. pombeCrb2P87074Phos73TEELSLtQLFEVP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...None
5155S. pombeCrb2P87074Phos80SLFEVPsQAAFAP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...None
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5156 rows × 32 columns

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" ], "text/plain": [ " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", "0 Human AANAT Q16613 Phos 31 T CQRRHtLPASE P63104 \n", "1 Human AATF Q9NY61 Phos 366 T VYRNRtLQKWH P19105 \n", "2 Human ABCG2 Q9UNQ0 Phos 362 T KKKKItVFKEI Q9UNQ0 \n", "3 Human ABI1 Q8IZP0 Phos 213 Y TVPNDyMTSPA P27986 \n", "4 Human ABI3 Q9P2A4 Phos 342 S VTRRYsDGWCE Q7L576 \n", "... ... ... ... ... ... .. ... ... \n", "5151 S. pombe Klp9 Q1MTQ7 Phos 605 S KKKVVsPIKPL Q9HDY1 \n", "5152 S. pombe Klp9 Q1MTQ7 Phos 611 S PIKPLsPSRRP Q9HDY1 \n", "5153 S. pombe Klp9 Q1MTQ7 Phos 613 S KPLSPsRRPPL Q9HDY1 \n", "5154 S. pombe Crb2 P87074 Phos 73 T EELSLtQLFEV P34208 \n", "5155 S. pombe Crb2 P87074 Phos 80 S LFEVPsQAAFA P34208 \n", "\n", " Int_gene Effect Method \\\n", "0 YWHAZ Enhance Molecular dynamics simulation(MD) \n", "1 MYL12A Inhibit Peptide pull-down \n", "2 ABCG2 Enhance Co-IP \n", "3 PIK3R1 Enhance Affinity capture binding assay \n", "4 CYFIP1 Inhibit Co-IP \n", "... ... ... ... \n", "5151 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5152 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5153 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5154 Chk1 Enhance Peptide pull-down \n", "5155 Chk1 Enhance Peptide pull-down \n", "\n", " Disease Co-localized PMID Co_localized \\\n", "0 NaN NaN 28387381 NaN \n", "1 Endometrial cancer NaN 22909821 NaN \n", "2 Prostate cancer Plasma membrane 18056989 Plasma membrane \n", "3 NaN NaN 20598684 NaN \n", "4 Thyroid cancer NaN 28978070 NaN \n", "... ... ... ... ... \n", "5151 NaN Spindle midzone 19686686 NaN \n", "5152 NaN Spindle midzone 19686686 NaN \n", "5153 NaN Spindle midzone 19686686 NaN \n", "5154 NaN NaN 22792081 NaN \n", "5155 NaN NaN 22792081 NaN \n", "\n", " Complex Origin Confidence PDBRES Score Interface Domain \\\n", "0 Complex2735 PyMOL Medium A31:THR 0.50 True NaN \n", "1 Complex3475 ZDOCK Low A366:THR 0.50 False AATF-Che1 \n", "2 Complex3607 PyMOL Medium A362:THR 0.50 False NaN \n", "3 Complex2954 ZDOCK Low B213:TYR 0.50 False NaN \n", "4 Complex3517 ZDOCK Low B342:SER 0.75 False SH3_9 \n", "... ... ... ... ... ... ... ... \n", "5151 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5152 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5153 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5154 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", "5155 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", "\n", " interface_sites_num \\\n", "0 {'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,... \n", "1 {'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,... \n", "2 {'A': '44,46,48,53,56,63,81,82,83,88,97,126,12... \n", "3 {'A': '1,363,364,365,620,621,622,625,626,627,6... \n", "4 {'A': '781,782,785,788,831,832,833,834,835,836... \n", "... ... \n", "5151 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5152 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5153 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5154 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", "5155 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", "\n", " interface_sequence_dict \\\n", "0 {'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E... \n", "1 {'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D... \n", "2 {'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q... \n", "3 {'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q... \n", "4 {'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F... \n", "... ... \n", "5151 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5152 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5153 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5154 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", "5155 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", "\n", " hf_complex_path \\\n", "0 ../data/ProteinStructures/Complexes/Complex273... \n", "1 ../data/ProteinStructures/Complexes/Complex347... \n", "2 ../data/ProteinStructures/Complexes/Complex360... \n", "3 ../data/ProteinStructures/Complexes/Complex295... \n", "4 ../data/ProteinStructures/Complexes/Complex351... \n", "... ... \n", "5151 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5152 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5153 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5154 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5155 ../data/ProteinStructures/Complexes/SP_Complex... \n", "\n", " Gene_sequence \\\n", "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... \n", "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... \n", "... ... \n", "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "\n", " Int_gene_sequence \\\n", "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... \n", "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", "... ... \n", "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", "\n", " Interactor_chain_1_from_complex \\\n", "0 A \n", "1 A \n", "2 A \n", "3 A \n", "4 A \n", "... ... \n", "5151 A \n", "5152 A \n", "5153 A \n", "5154 A \n", "5155 A \n", "\n", " Interactor_1_seq_from_complex \\\n", "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", "... ... \n", "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "\n", " Interactor_chain_2_from_complex \\\n", "0 B \n", "1 B \n", "2 B \n", "3 B \n", "4 B \n", "... ... \n", "5151 B \n", "5152 B \n", "5153 B \n", "5154 B \n", "5155 B \n", "\n", " Interactor_2_seq_from_complex Alternative_Complex \n", "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... None \n", "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... None \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... None \n", "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... None \n", "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... None \n", "... ... ... \n", "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", "\n", "[5156 rows x 32 columns]" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import numpy as np\n", "\n", "def check_interface_site(row):\n", "\n", " site = int(row[\"Site\"])\n", " aminoa = from AA\n", " sites_dict = row[\"interface_sites_num\"]\n", "\n", " if pd.isna(sites_dict) or sites_dict == \"\" or sites_dict == {}:\n", " return np.nan\n", "\n", " pdbres = row[\"PDBRES\"]\n", "\n", " # ---- case 1: PDBRES exists → use that chain ----\n", " if isinstance(pdbres, str) and pdbres != \"\":\n", " chain = pdbres[0] # first letter\n", "\n", " if chain not in sites_dict:\n", " return \"False\"\n", "\n", " sites = sites_dict[chain]\n", "\n", " if isinstance(sites, str):\n", " sites = [int(x) for x in sites.split(\",\")]\n", "\n", " if site in sites:\n", " return \"True\"\n", " else:\n", " return \"False\"\n", "\n", " # ---- case 2: PDBRES missing → check all chains ----\n", " else:\n", "\n", " for chain, sites in sites_dict.items():\n", "\n", " if isinstance(sites, str):\n", " sites = [int(x) for x in sites.split(\",\")]\n", "\n", " if site in sites:\n", " #check if amino acid aminoa is the same as the one from the site detected. can be obtained from dictionary from row[\"interface_sequence_dict\"]\n", " return \"Possibly\"\n", "\n", " return \"False\"\n", "\n", "df[\"site_in_interface\"] = df.apply(check_interface_site, axis=1)" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffectMethodDiseaseCo-localizedPMIDCo_localizedComplexOriginConfidencePDBRESScoreInterfaceDomaininterface_sites_numinterface_sequence_dicthf_complex_pathGene_sequenceInt_gene_sequenceInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexAlternative_Complexsite_in_interface
0HumanAANATQ16613Phos31TCQRRHtLPASEP63104YWHAZEnhanceMolecular dynamics simulation(MD)NaNNaN28387381NaNComplex2735PyMOLMediumA31:THR0.50TrueNaN{'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,...{'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E...../data/ProteinStructures/Complexes/Complex273...MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...AMSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...BMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...NoneTrue
1HumanAATFQ9NY61Phos366TVYRNRtLQKWHP19105MYL12AInhibitPeptide pull-downEndometrial cancerNaN22909821NaNComplex3475ZDOCKLowA366:THR0.50FalseAATF-Che1{'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,...{'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D...../data/ProteinStructures/Complexes/Complex347...MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...AMAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...BMSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...NoneFalse
2HumanABCG2Q9UNQ0Phos362TKKKKItVFKEIQ9UNQ0ABCG2EnhanceCo-IPProstate cancerPlasma membrane18056989Plasma membraneComplex3607PyMOLMediumA362:THR0.50FalseNaN{'A': '44,46,48,53,56,63,81,82,83,88,97,126,12...{'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q...../data/ProteinStructures/Complexes/Complex360...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...AMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...BMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...NoneFalse
3HumanABI1Q8IZP0Phos213YTVPNDyMTSPAP27986PIK3R1EnhanceAffinity capture binding assayNaNNaN20598684NaNComplex2954ZDOCKLowB213:TYR0.50FalseNaN{'A': '1,363,364,365,620,621,622,625,626,627,6...{'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q...../data/ProteinStructures/Complexes/Complex295...MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...AMSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...BMAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...NoneFalse
4HumanABI3Q9P2A4Phos342SVTRRYsDGWCEQ7L576CYFIP1InhibitCo-IPThyroid cancerNaN28978070NaNComplex3517ZDOCKLowB342:SER0.75FalseSH3_9{'A': '781,782,785,788,831,832,833,834,835,836...{'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F...../data/ProteinStructures/Complexes/Complex351...MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...AMAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...BMAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...NoneFalse
......................................................................................................
5151S. pombeKlp9Q1MTQ7Phos605SKKKVVsPIKPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5152S. pombeKlp9Q1MTQ7Phos611SPIKPLsPSRRPQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5153S. pombeKlp9Q1MTQ7Phos613SKPLSPsRRPPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5154S. pombeCrb2P87074Phos73TEELSLtQLFEVP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
5155S. pombeCrb2P87074Phos80SLFEVPsQAAFAP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
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5156 rows × 33 columns

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" ], "text/plain": [ " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", "0 Human AANAT Q16613 Phos 31 T CQRRHtLPASE P63104 \n", "1 Human AATF Q9NY61 Phos 366 T VYRNRtLQKWH P19105 \n", "2 Human ABCG2 Q9UNQ0 Phos 362 T KKKKItVFKEI Q9UNQ0 \n", "3 Human ABI1 Q8IZP0 Phos 213 Y TVPNDyMTSPA P27986 \n", "4 Human ABI3 Q9P2A4 Phos 342 S VTRRYsDGWCE Q7L576 \n", "... ... ... ... ... ... .. ... ... \n", "5151 S. pombe Klp9 Q1MTQ7 Phos 605 S KKKVVsPIKPL Q9HDY1 \n", "5152 S. pombe Klp9 Q1MTQ7 Phos 611 S PIKPLsPSRRP Q9HDY1 \n", "5153 S. pombe Klp9 Q1MTQ7 Phos 613 S KPLSPsRRPPL Q9HDY1 \n", "5154 S. pombe Crb2 P87074 Phos 73 T EELSLtQLFEV P34208 \n", "5155 S. pombe Crb2 P87074 Phos 80 S LFEVPsQAAFA P34208 \n", "\n", " Int_gene Effect Method \\\n", "0 YWHAZ Enhance Molecular dynamics simulation(MD) \n", "1 MYL12A Inhibit Peptide pull-down \n", "2 ABCG2 Enhance Co-IP \n", "3 PIK3R1 Enhance Affinity capture binding assay \n", "4 CYFIP1 Inhibit Co-IP \n", "... ... ... ... \n", "5151 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5152 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5153 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5154 Chk1 Enhance Peptide pull-down \n", "5155 Chk1 Enhance Peptide pull-down \n", "\n", " Disease Co-localized PMID Co_localized \\\n", "0 NaN NaN 28387381 NaN \n", "1 Endometrial cancer NaN 22909821 NaN \n", "2 Prostate cancer Plasma membrane 18056989 Plasma membrane \n", "3 NaN NaN 20598684 NaN \n", "4 Thyroid cancer NaN 28978070 NaN \n", "... ... ... ... ... \n", "5151 NaN Spindle midzone 19686686 NaN \n", "5152 NaN Spindle midzone 19686686 NaN \n", "5153 NaN Spindle midzone 19686686 NaN \n", "5154 NaN NaN 22792081 NaN \n", "5155 NaN NaN 22792081 NaN \n", "\n", " Complex Origin Confidence PDBRES Score Interface Domain \\\n", "0 Complex2735 PyMOL Medium A31:THR 0.50 True NaN \n", "1 Complex3475 ZDOCK Low A366:THR 0.50 False AATF-Che1 \n", "2 Complex3607 PyMOL Medium A362:THR 0.50 False NaN \n", "3 Complex2954 ZDOCK Low B213:TYR 0.50 False NaN \n", "4 Complex3517 ZDOCK Low B342:SER 0.75 False SH3_9 \n", "... ... ... ... ... ... ... ... \n", "5151 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5152 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5153 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5154 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", "5155 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", "\n", " interface_sites_num \\\n", "0 {'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,... \n", "1 {'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,... \n", "2 {'A': '44,46,48,53,56,63,81,82,83,88,97,126,12... \n", "3 {'A': '1,363,364,365,620,621,622,625,626,627,6... \n", "4 {'A': '781,782,785,788,831,832,833,834,835,836... \n", "... ... \n", "5151 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5152 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5153 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5154 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", "5155 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", "\n", " interface_sequence_dict \\\n", "0 {'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E... \n", "1 {'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D... \n", "2 {'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q... \n", "3 {'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q... \n", "4 {'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F... \n", "... ... \n", "5151 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5152 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5153 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5154 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", "5155 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", "\n", " hf_complex_path \\\n", "0 ../data/ProteinStructures/Complexes/Complex273... \n", "1 ../data/ProteinStructures/Complexes/Complex347... \n", "2 ../data/ProteinStructures/Complexes/Complex360... \n", "3 ../data/ProteinStructures/Complexes/Complex295... \n", "4 ../data/ProteinStructures/Complexes/Complex351... \n", "... ... \n", "5151 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5152 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5153 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5154 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5155 ../data/ProteinStructures/Complexes/SP_Complex... \n", "\n", " Gene_sequence \\\n", "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... \n", "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... \n", "... ... \n", "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "\n", " Int_gene_sequence \\\n", "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... \n", "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", "... ... \n", "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", "\n", " Interactor_chain_1_from_complex \\\n", "0 A \n", "1 A \n", "2 A \n", "3 A \n", "4 A \n", "... ... \n", "5151 A \n", "5152 A \n", "5153 A \n", "5154 A \n", "5155 A \n", "\n", " Interactor_1_seq_from_complex \\\n", "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", "... ... \n", "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "\n", " Interactor_chain_2_from_complex \\\n", "0 B \n", "1 B \n", "2 B \n", "3 B \n", "4 B \n", "... ... \n", "5151 B \n", "5152 B \n", "5153 B \n", "5154 B \n", "5155 B \n", "\n", " Interactor_2_seq_from_complex Alternative_Complex \\\n", "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... None \n", "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... None \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... None \n", "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... None \n", "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... None \n", "... ... ... \n", "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", "\n", " site_in_interface \n", "0 True \n", "1 False \n", "2 False \n", "3 False \n", "4 False \n", "... ... \n", "5151 False \n", "5152 False \n", "5153 False \n", "5154 False \n", "5155 False \n", "\n", "[5156 rows x 33 columns]" ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[1468, 1469, 1470, 1473, 1474, 1476, 1477, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1487, 1488, 1489, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510, 1511, 1512, 1513, 1514, 1516, 1517, 1518, 1519, 1521, 1522, 1525, 1527, 1528, 1529]\n", "APC ['K', 'Q', 'A', 'N', 'A', 'V', 'Q', 'Q', 'V', 'L', 'P', 'D', 'A', 'D', 'X', 'L', 'L', 'H', 'F', 'A', 'T', 'E', 'S', 'T', 'S', 'X', 'X', 'L', 'X', 'A', 'L', 'X', 'L', 'D', 'E', 'P', 'I', 'Q', 'K', 'D', 'E', 'L', 'M', 'P', 'V', 'Q']\n", "Mismatch | Gene=APC | Site=1505 | Expected=S | Found=X\n", "[1468, 1469, 1470, 1473, 1474, 1476, 1477, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1487, 1488, 1489, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510, 1511, 1512, 1513, 1514, 1516, 1517, 1518, 1519, 1521, 1522, 1525, 1527, 1528, 1529]\n", "APC ['K', 'Q', 'A', 'N', 'A', 'V', 'Q', 'Q', 'V', 'L', 'P', 'D', 'A', 'D', 'X', 'L', 'L', 'H', 'F', 'A', 'T', 'E', 'S', 'T', 'S', 'X', 'X', 'L', 'X', 'A', 'L', 'X', 'L', 'D', 'E', 'P', 'I', 'Q', 'K', 'D', 'E', 'L', 'M', 'P', 'V', 'Q']\n", "Mismatch | Gene=APC | Site=1507 | Expected=S | Found=X\n", "[764, 765, 767, 768, 769, 770, 772]\n", "CFTR ['R', 'R', 'Q', 'X', 'V', 'L', 'L']\n", "Mismatch | Gene=CFTR | Site=768 | Expected=S | Found=X\n", "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", "Mismatch | Gene=ERRFI1 | Site=394 | Expected=Y | Found=X\n", "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", "Mismatch | Gene=ERRFI1 | Site=394 | Expected=Y | Found=X\n", "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", "Mismatch | Gene=ERRFI1 | Site=395 | Expected=Y | Found=X\n", "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", "Mismatch | Gene=ERRFI1 | Site=395 | Expected=Y | Found=X\n", "[695, 699, 702, 703, 704, 706, 707, 709, 710, 711, 712, 725, 727, 728, 730, 731, 732, 733, 734, 1045, 1046, 1049, 1052, 1053, 1056, 1061, 1062, 1063, 1064, 1065, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1106, 1107, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1121, 1122, 1125, 1126, 1127, 1128, 1129, 1130, 1131, 1132, 1383, 1385, 1386, 1387, 1388, 1389, 1390, 1391]\n", "ESPL1 ['E', 'R', 'R', 'A', 'Q', 'P', 'G', 'L', 'E', 'E', 'F', 'E', 'R', 'F', 'Y', 'S', 'N', 'I', 'A', 'D', 'L', 'S', 'Q', 'Q', 'F', 'C', 'T', 'E', 'F', 'G', 'E', 'L', 'F', 'L', 'R', 'G', 'P', 'L', 'E', 'V', 'A', 'T', 'V', 'A', 'K', 'E', 'P', 'G', 'P', 'I', 'P', 'S', 'S', 'X', 'P', 'V', 'L', 'K', 'T', 'K', 'V', 'Q', 'R', 'V', 'Q', 'T', 'R', 'L']\n", "Mismatch | Gene=ESPL1 | Site=1126 | Expected=S | Found=X\n" ] } ], "source": [ "import pandas as pd\n", "import numpy as np\n", "\n", "def check_interface_site(row):\n", "\n", " site = int(row[\"Site\"])\n", " aminoa = row[\"AA\"]\n", " sites_dict = row[\"interface_sites_num\"]\n", " seq_dict = row[\"interface_sequence_dict\"]\n", "\n", " if pd.isna(sites_dict) or sites_dict == \"\" or sites_dict == {}:\n", " return np.nan\n", "\n", " pdbres = row[\"PDBRES\"]\n", "\n", " # ---- case 1: PDBRES exists → use that chain ----\n", " if isinstance(pdbres, str) and pdbres != \"\":\n", " chain = pdbres[0] # first letter\n", "\n", " if chain not in sites_dict:\n", " return \"False\"\n", "\n", " sites = sites_dict[chain]\n", " seq = seq_dict[chain]\n", " if isinstance(sites, str):\n", " sites = [int(x) for x in sites.split(\",\")]\n", "\n", " if isinstance(seq, str):\n", " seq = [str(x) for x in seq.split(\",\")]\n", "\n", " if site in sites:\n", " idx = sites.index(site)\n", " aa_interface = seq[idx]\n", "\n", " if aa_interface.upper() == aminoa.upper():\n", " return \"True\"\n", " else:\n", " print(sites)\n", " print(row['Gene'], seq)\n", " print(f\"Mismatch | Gene={row['Gene']} | Site={site} | Expected={aminoa} | Found={aa_interface}\")\n", " return \"False\"\n", " else:\n", " return \"False\"\n", "\n", " # ---- case 2: PDBRES missing → check all chains ----\n", " else:\n", " found = False\n", " for chain, sites in sites_dict.items():\n", " if isinstance(sites, str):\n", " sites = [int(x) for x in sites.split(\",\")]\n", "\n", " if site in sites:\n", " seq = seq_dict[chain]\n", "\n", " if isinstance(seq, str):\n", " seq = [str(x) for x in seq.split(\",\")]\n", "\n", " idx = sites.index(site)\n", " aa_interface = seq[idx]\n", "\n", " if aa_interface.upper() == aminoa.upper():\n", " found = True\n", " return \"True\"\n", " if found:\n", " print(f\"Gene={row['Gene']} | Site={site} | Expected={aminoa} | Found={aa_interface} | COMPLEX={row['Complex']}\")\n", " print(f'found in chain {chain}')\n", " return \"False\"\n", "\n", "df[\"site_in_interface\"] = df.apply(check_interface_site, axis=1)" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffectMethodDiseaseCo-localizedPMIDCo_localizedComplexOriginConfidencePDBRESScoreInterfaceDomaininterface_sites_numinterface_sequence_dicthf_complex_pathGene_sequenceInt_gene_sequenceInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexAlternative_Complexsite_in_interface
0HumanAANATQ16613Phos31TCQRRHtLPASEP63104YWHAZEnhanceMolecular dynamics simulation(MD)NaNNaN28387381NaNComplex2735PyMOLMediumA31:THR0.50TrueNaN{'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,...{'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E...../data/ProteinStructures/Complexes/Complex273...MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...AMSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...BMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...NoneTrue
1HumanAATFQ9NY61Phos366TVYRNRtLQKWHP19105MYL12AInhibitPeptide pull-downEndometrial cancerNaN22909821NaNComplex3475ZDOCKLowA366:THR0.50FalseAATF-Che1{'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,...{'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D...../data/ProteinStructures/Complexes/Complex347...MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...AMAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...BMSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...NoneFalse
2HumanABCG2Q9UNQ0Phos362TKKKKItVFKEIQ9UNQ0ABCG2EnhanceCo-IPProstate cancerPlasma membrane18056989Plasma membraneComplex3607PyMOLMediumA362:THR0.50FalseNaN{'A': '44,46,48,53,56,63,81,82,83,88,97,126,12...{'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q...../data/ProteinStructures/Complexes/Complex360...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...AMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...BMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...NoneFalse
3HumanABI1Q8IZP0Phos213YTVPNDyMTSPAP27986PIK3R1EnhanceAffinity capture binding assayNaNNaN20598684NaNComplex2954ZDOCKLowB213:TYR0.50FalseNaN{'A': '1,363,364,365,620,621,622,625,626,627,6...{'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q...../data/ProteinStructures/Complexes/Complex295...MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...AMSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...BMAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...NoneFalse
4HumanABI3Q9P2A4Phos342SVTRRYsDGWCEQ7L576CYFIP1InhibitCo-IPThyroid cancerNaN28978070NaNComplex3517ZDOCKLowB342:SER0.75FalseSH3_9{'A': '781,782,785,788,831,832,833,834,835,836...{'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F...../data/ProteinStructures/Complexes/Complex351...MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...AMAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...BMAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...NoneFalse
......................................................................................................
5151S. pombeKlp9Q1MTQ7Phos605SKKKVVsPIKPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5152S. pombeKlp9Q1MTQ7Phos611SPIKPLsPSRRPQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5153S. pombeKlp9Q1MTQ7Phos613SKPLSPsRRPPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5154S. pombeCrb2P87074Phos73TEELSLtQLFEVP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
5155S. pombeCrb2P87074Phos80SLFEVPsQAAFAP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
\n", "

5156 rows × 33 columns

\n", "
" ], "text/plain": [ " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", "0 Human AANAT Q16613 Phos 31 T CQRRHtLPASE P63104 \n", "1 Human AATF Q9NY61 Phos 366 T VYRNRtLQKWH P19105 \n", "2 Human ABCG2 Q9UNQ0 Phos 362 T KKKKItVFKEI Q9UNQ0 \n", "3 Human ABI1 Q8IZP0 Phos 213 Y TVPNDyMTSPA P27986 \n", "4 Human ABI3 Q9P2A4 Phos 342 S VTRRYsDGWCE Q7L576 \n", "... ... ... ... ... ... .. ... ... \n", "5151 S. pombe Klp9 Q1MTQ7 Phos 605 S KKKVVsPIKPL Q9HDY1 \n", "5152 S. pombe Klp9 Q1MTQ7 Phos 611 S PIKPLsPSRRP Q9HDY1 \n", "5153 S. pombe Klp9 Q1MTQ7 Phos 613 S KPLSPsRRPPL Q9HDY1 \n", "5154 S. pombe Crb2 P87074 Phos 73 T EELSLtQLFEV P34208 \n", "5155 S. pombe Crb2 P87074 Phos 80 S LFEVPsQAAFA P34208 \n", "\n", " Int_gene Effect Method \\\n", "0 YWHAZ Enhance Molecular dynamics simulation(MD) \n", "1 MYL12A Inhibit Peptide pull-down \n", "2 ABCG2 Enhance Co-IP \n", "3 PIK3R1 Enhance Affinity capture binding assay \n", "4 CYFIP1 Inhibit Co-IP \n", "... ... ... ... \n", "5151 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5152 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5153 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", "5154 Chk1 Enhance Peptide pull-down \n", "5155 Chk1 Enhance Peptide pull-down \n", "\n", " Disease Co-localized PMID Co_localized \\\n", "0 NaN NaN 28387381 NaN \n", "1 Endometrial cancer NaN 22909821 NaN \n", "2 Prostate cancer Plasma membrane 18056989 Plasma membrane \n", "3 NaN NaN 20598684 NaN \n", "4 Thyroid cancer NaN 28978070 NaN \n", "... ... ... ... ... \n", "5151 NaN Spindle midzone 19686686 NaN \n", "5152 NaN Spindle midzone 19686686 NaN \n", "5153 NaN Spindle midzone 19686686 NaN \n", "5154 NaN NaN 22792081 NaN \n", "5155 NaN NaN 22792081 NaN \n", "\n", " Complex Origin Confidence PDBRES Score Interface Domain \\\n", "0 Complex2735 PyMOL Medium A31:THR 0.50 True NaN \n", "1 Complex3475 ZDOCK Low A366:THR 0.50 False AATF-Che1 \n", "2 Complex3607 PyMOL Medium A362:THR 0.50 False NaN \n", "3 Complex2954 ZDOCK Low B213:TYR 0.50 False NaN \n", "4 Complex3517 ZDOCK Low B342:SER 0.75 False SH3_9 \n", "... ... ... ... ... ... ... ... \n", "5151 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5152 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5153 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", "5154 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", "5155 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", "\n", " interface_sites_num \\\n", "0 {'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,... \n", "1 {'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,... \n", "2 {'A': '44,46,48,53,56,63,81,82,83,88,97,126,12... \n", "3 {'A': '1,363,364,365,620,621,622,625,626,627,6... \n", "4 {'A': '781,782,785,788,831,832,833,834,835,836... \n", "... ... \n", "5151 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5152 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5153 {'A': '336,339,340,342,343,345,362,363,365,366... \n", "5154 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", "5155 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", "\n", " interface_sequence_dict \\\n", "0 {'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E... \n", "1 {'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D... \n", "2 {'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q... \n", "3 {'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q... \n", "4 {'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F... \n", "... ... \n", "5151 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5152 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5153 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", "5154 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", "5155 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", "\n", " hf_complex_path \\\n", "0 ../data/ProteinStructures/Complexes/Complex273... \n", "1 ../data/ProteinStructures/Complexes/Complex347... \n", "2 ../data/ProteinStructures/Complexes/Complex360... \n", "3 ../data/ProteinStructures/Complexes/Complex295... \n", "4 ../data/ProteinStructures/Complexes/Complex351... \n", "... ... \n", "5151 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5152 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5153 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5154 ../data/ProteinStructures/Complexes/SP_Complex... \n", "5155 ../data/ProteinStructures/Complexes/SP_Complex... \n", "\n", " Gene_sequence \\\n", "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... \n", "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... \n", "... ... \n", "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "\n", " Int_gene_sequence \\\n", "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... \n", "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", "... ... \n", "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", "\n", " Interactor_chain_1_from_complex \\\n", "0 A \n", "1 A \n", "2 A \n", "3 A \n", "4 A \n", "... ... \n", "5151 A \n", "5152 A \n", "5153 A \n", "5154 A \n", "5155 A \n", "\n", " Interactor_1_seq_from_complex \\\n", "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", "... ... \n", "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", "\n", " Interactor_chain_2_from_complex \\\n", "0 B \n", "1 B \n", "2 B \n", "3 B \n", "4 B \n", "... ... \n", "5151 B \n", "5152 B \n", "5153 B \n", "5154 B \n", "5155 B \n", "\n", " Interactor_2_seq_from_complex Alternative_Complex \\\n", "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... None \n", "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... None \n", "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... None \n", "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... None \n", "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... None \n", "... ... ... \n", "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", "\n", " site_in_interface \n", "0 True \n", "1 False \n", "2 False \n", "3 False \n", "4 False \n", "... ... \n", "5151 False \n", "5152 False \n", "5153 False \n", "5154 False \n", "5155 False \n", "\n", "[5156 rows x 33 columns]" ] }, "execution_count": 34, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pd.set_option('display.max_colwidth', None)\n", "df" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [], "source": [ "df.to_csv(\"../data/ptmint_final.csv\", index=False)" ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [ { "data": { "image/png": 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", "text/plain": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import matplotlib.pyplot as plt\n", "\n", "counts = df[\"site_in_interface\"].value_counts(dropna=False)\n", "\n", "counts.plot(kind=\"bar\")\n", "\n", "plt.xlabel(\"Site in Interface\")\n", "plt.ylabel(\"Count\")\n", "plt.title(\"Distribution of PTM Sites in Interface\")\n", "plt.xticks(rotation=0)\n", "\n", "plt.show()" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.18" } }, "nbformat": 4, "nbformat_minor": 2 }