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"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/github/sokrypton/ColabDesign/blob/v1.1.1/af/examples/disulfide_design.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "YRk_XS2NILil"
},
"source": [
"# disulfide-hallucination\n",
"For a given length, generate/hallucinate a disulfide-rich sequence that AlphaFold thinks folds into a well structured protein"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"cellView": "form",
"id": "-AXy0s_4cKaK"
},
"outputs": [],
"source": [
"#@title setup\n",
"%%time\n",
"import os\n",
"if not os.path.isdir(\"params\"):\n",
" # get code\n",
" os.system(\"pip -q install git+https://github.com/sokrypton/ColabDesign.git@v1.1.1\")\n",
" # for debugging\n",
" os.system(\"ln -s /usr/local/lib/python3.*/dist-packages/colabdesign colabdesign\")\n",
" # download params\n",
" os.system(\"mkdir params\")\n",
" os.system(\"apt-get install aria2 -qq\")\n",
" os.system(\"aria2c -q -x 16 https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar\")\n",
" os.system(\"tar -xf alphafold_params_2022-12-06.tar -C params\")\n",
"\n",
"import warnings\n",
"warnings.simplefilter(action='ignore', category=FutureWarning)\n",
"\n",
"import os\n",
"from colabdesign import mk_afdesign_model, clear_mem\n",
"from IPython.display import HTML\n",
"from google.colab import files\n",
"import numpy as np\n",
"\n",
"def get_pdb(pdb_code=\"\"):\n",
" if pdb_code is None or pdb_code == \"\":\n",
" upload_dict = files.upload()\n",
" pdb_string = upload_dict[list(upload_dict.keys())[0]]\n",
" with open(\"tmp.pdb\",\"wb\") as out: out.write(pdb_string)\n",
" return \"tmp.pdb\"\n",
" elif os.path.isfile(pdb_code):\n",
" return pdb_code\n",
" elif len(pdb_code) == 4:\n",
" os.system(f\"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb\")\n",
" return f\"{pdb_code}.pdb\"\n",
" else:\n",
" os.system(f\"wget -qnc https://alphafold.ebi.ac.uk/files/AF-{pdb_code}-F1-model_v3.pdb\")\n",
" return f\"AF-{pdb_code}-F1-model_v3.pdb\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "7JbLyVu4ILil"
},
"outputs": [],
"source": [
"import random\n",
"from jax.lax import dynamic_slice\n",
"import jax.numpy as jnp\n",
"\n",
"from colabdesign.af.loss import _get_con_loss\n",
"def get_con_loss(dgram, dgram_bins, cutoff=None, binary=True,\n",
" num=1, seqsep=0, offset=None):\n",
" '''convert distogram into contact loss''' \n",
" x = _get_con_loss(dgram, dgram_bins, cutoff, binary) \n",
" a,b = x.shape\n",
" if offset is None:\n",
" mask = jnp.abs(jnp.arange(a)[:,None] - jnp.arange(b)[None,:]) >= seqsep\n",
" else:\n",
" mask = jnp.abs(offset) >= seqsep\n",
" x = jnp.sort(jnp.where(mask,x,jnp.nan))\n",
" k_mask = (jnp.arange(b) < num) * (jnp.isnan(x) == False) \n",
" return jnp.where(k_mask,x,0.0).sum(-1) / (k_mask.sum(-1) + 1e-8)\n",
"\n",
"def generate_disulfide_pattern(L, disulfide_num, min_sep=5):\n",
" disulfide_pattern = []\n",
" positions = list(range(L))\n",
" for n in range(disulfide_num):\n",
" for _ in range(100): # try 100 time per postion.\n",
" i,j = random.sample(positions, k=2)\n",
" if abs(i-j)<=min_sep: continue # set min loop len.\n",
" positions.remove(i)\n",
" positions.remove(j)\n",
" disulfide_pattern.append((i,j))\n",
" # check\n",
" if _ > 99:\n",
" print('Not find good disulfide_pos! exit....')\n",
" return 0 # not good pose!\n",
" else:\n",
" break\n",
" sequence_pattern = list('X'*L)\n",
" for pair in disulfide_pattern:\n",
" for i in pair: sequence_pattern[i] = 'C'\n",
"\n",
" return disulfide_pattern, ''.join(sequence_pattern), L\n",
"\n",
"def disulfide_loss(inputs, outputs):\n",
" def get_disulfide_loss(dgram, dgram_bins, disulfide_pattern):\n",
" '''\n",
" Func: simple disulfide loss, make the contacts < 7.0/7.5A.\n",
" # see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316719/\n",
" params: disulfide_pattern: List[(pos1, pos2), (pos3, pos4)...]\n",
" '''\n",
" disulfide_loss = 0.0\n",
" for pair in disulfide_pattern:\n",
" i,j = pair\n",
" pair_dgram = dynamic_slice(dgram, (i,j,0), (1,1,len(dgram_bins))) + dynamic_slice(dgram, (j,i,0), (1,1,len(dgram_bins)))\n",
" disulfide_loss += get_con_loss(pair_dgram, dgram_bins, cutoff=7.0, binary=False, num=1)\n",
" return disulfide_loss.mean()\n",
"\n",
" # add disulfide loss here:\n",
" dgram_logits = outputs['distogram']['logits']\n",
" dgram_bins = jnp.append(0, outputs[\"distogram\"][\"bin_edges\"])\n",
" return {\"disulfide\":get_disulfide_loss(dgram_logits, dgram_bins, inputs['opt']['disulfide_pattern'])}"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "aU4e-ZkfILim"
},
"source": [
"0. generate_cys_pattern"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "vrSatV2sILim"
},
"outputs": [],
"source": [
"disulfide_pattern, sequence_pattern, L = generate_disulfide_pattern(35, 3)\n",
"print(disulfide_pattern)\n",
"print(sequence_pattern)\n",
"print(L)"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "jGNGjHeyILim"
},
"source": [
"1. hallucination with disulfide-pattern"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "HmsBDNhmILin"
},
"outputs": [],
"source": [
"# using some disulfide sequence as input:\n",
"clear_mem()\n",
"af_model = mk_afdesign_model(protocol=\"hallucination\", loss_callback=disulfide_loss)\n",
"af_model.opt[\"weights\"][\"disulfide\"] = 1.0\n",
"af_model.prep_inputs(length=L)\n",
"\n",
"print(\"length\",af_model._len)\n",
"print(\"weights\",af_model.opt[\"weights\"])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "MmBtBMnBILin"
},
"outputs": [],
"source": [
"# set disulfide_pattern sequence.\n",
"af_model.restart(seq=sequence_pattern, add_seq=True, rm_aa='C')\n",
"# set disulfide_pattern:\n",
"af_model.opt['disulfide_pattern'] = disulfide_pattern\n",
"# reweight con:\n",
"af_model.opt[\"weights\"]['con'] = 0.5"
]
},
{
"cell_type": "code",
"source": [
"af_model.design_3stage(50,50,10)"
],
"metadata": {
"id": "wstI0n4zMydi"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "ewlj8671ILio"
},
"outputs": [],
"source": [
"af_model.save_pdb(f\"{af_model.protocol}.pdb\")\n",
"af_model.plot_pdb(show_sidechains=True)"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "iVEqJKaKILio"
},
"source": [
"2. fix-sidechain with pyRosetta"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "VGwyvaodILio"
},
"outputs": [],
"source": [
"from pyrosetta import init, pose_from_pdb, Pose, create_score_function\n",
"from pyrosetta.rosetta.protocols.relax import FastRelax\n",
"from pyrosetta.rosetta.core.pack.task import TaskFactory\n",
"from pyrosetta.rosetta.core.kinematics import MoveMap\n",
"from pyrosetta.rosetta.core.pack.task.operation import InitializeFromCommandline\n",
"from pyrosetta.rosetta.protocols.denovo_design import DisulfidizeMover\n",
"from pyrosetta.rosetta.core.pack.task.operation import RestrictToRepacking\n",
"from pyrosetta.rosetta.core.select.residue_selector import ChainSelector\n",
"\n",
"def fastrelax(pose):\n",
" full_score = create_score_function('ref2015')\n",
" tf = TaskFactory()\n",
" # tf.push_back(InitializeFromCommandline())\n",
" tf.push_back(RestrictToRepacking())\n",
" mmap = MoveMap()\n",
" mmap.set_bb(True)\n",
" mmap.set_chi(True)\n",
"\n",
" # FastRelax:\n",
" fast_design = FastRelax(full_score, 4) # repeat:6\n",
" fast_design.set_task_factory(tf)\n",
" fast_design.set_movemap(mmap)\n",
" fast_design.apply(pose)\n",
" \n",
"def build_stapled_pose(pose, cys_pattern):\n",
" # rebuild \n",
" disulfidizer = DisulfidizeMover()\n",
" disulfidizer.set_match_rt_limit(999.0)\n",
" disulfidizer.set_max_disulf_score(999.0)\n",
" for pair in cys_pattern:\n",
" full_score = create_score_function('ref2015')\n",
" stapled_pose = Pose().assign(pose) # pose for disulfides stapled\n",
" residue1, residue2 = pair\n",
" disulfidizer.make_disulfide(stapled_pose, residue1+1, residue2+1, False, full_score)\n",
" # fastdesign mover\n",
" pdbnum1 = stapled_pose.pdb_info().pose2pdb(residue1)\n",
" pdbnum2 = stapled_pose.pdb_info().pose2pdb(residue2)\n",
" print('# OPTIMIZE: Around These Residues: %s %s' % (pdbnum1, pdbnum2))\n",
"\n",
" # save pdb:\n",
" fastrelax(stapled_pose)\n",
" \n",
" # filter: all stapled?\n",
" v = ChainSelector(1).apply(stapled_pose)\n",
" l = disulfidizer.find_current_disulfides(stapled_pose, v, v)\n",
" print(len([i for i in l]), len(cys_pattern))\n",
" if len([i for i in l]) == len(cys_pattern):\n",
" return stapled_pose\n",
" else:\n",
" return 0\n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "zhMey-4lILip"
},
"outputs": [],
"source": [
"# optimze the side-chain\n",
"init('-mute all')\n",
"pose = pose_from_pdb(f\"{af_model.protocol}.pdb\")\n",
"stapled_pose = build_stapled_pose(pose, disulfide_pattern)"
]
}
],
"metadata": {
"accelerator": "GPU",
"colab": {
"collapsed_sections": [
"q4qiU9I0QHSz"
],
"name": "disulfide_design.ipynb",
"provenance": [],
"include_colab_link": true
},
"kernelspec": {
"display_name": "Python 3.8.10 64-bit",
"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": "3.8.10"
},
"vscode": {
"interpreter": {
"hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
}
}
},
"nbformat": 4,
"nbformat_minor": 0
} |