dynotx/synthetic_dimers

Dyno Synthetic Dimer Dataset

The datasets in this repo were used to train Dyno Psi-0 and Dyno Psi-1. This dataset was curated using predicted protein structures from the AlphaFold Protein Structure Database, subset to entries from AFDB50. Dimers were curated by using domain annotations from the TED domain annotations provided by the CATH database to identify domains within the same monomer structure that share an interface. These were further clustered using Foldseek to produce cluster representatives. A further refined set of dimers was identified by refolding all the cluster representatives with AlphaFold2, filtering by interface metrics, and refined using PyRosetta FastRelax. For more information on how this dataset was generated and used, please see our white paper.

Summary

This dataset contains the three compressed archives along with an index file. Be aware that two of the archives contain a large number of files, and the full dataset takes up ~800GB of disk space. Consider only downloading the cluster representatives or the AF2-filtered set if you don't need the full set.

The archives contain structure files for each synthetic dimer. Each dimer is assigned an ID based on the AFDB entry it came from along with the TED-annotated domains that constitute the chains of the synthetic dimer (e.g. AF-A0A0B7FL75-F1-model_v4_TED01_TED02). The structure files each have two protein chains, A and B, corresponding to these two domains.

Name	Description	Number of files	Uncompressed size
cifs_cluster_reps.tar.gz	MMCIF files for the cluster representatives	1063207	198 GB
cifs_noncluster_reps.tar.gz	MMCIF files for the other dimers that are not cluster reps	3007752	605 GB
pdbs_filtered_relaxed.tar.gz	PDB files for the cluster reps that pass additional AF2 refolding filters and were further relaxed with PyRosetta FastRelax	32253	10 GB

index_df.tsv fields:

Field	Description	Example
dimer_id	{afdb_id}_{domain_id1}\_{domain_id2}	AF-A0A0B7FL75-F1-model_v4_TED01_TED02
cluster_rep	the dimer_id of the cluster representative for the cluster this dimer belongs to	AF-A0A0B7FL75-F1-model_v4_TED01_TED02
is_cluster_rep	whether or not this dimer is a cluster representative	True
afdb_id	the AFDB ID of the original monomer	AF-A0A0B7FL75-F1-model_v4
start_{1/2}	the start index of the 1st/2nd domain in the original monomer, 1-indexed	5
end_{1/2}	the end index of the 1st/2nd domain in the original monomer, 1-indexed	145
num_res_{1/2}	the length of the 1st/2nd domain	141
num_interface_res_{1/2}	the number of residues in the 1st/2nd domain for which the CA is within 10Å of a CA in the other domain	14
interface_idxs_{1/2}	indices of the interface residues in the 1st/2nd domain, 1-indexed relative to the full-length monomer	10,11,12,14,94,96,97,100,129,130,131,132,133,134
total_length	total length of the dimer	370
pass_af2_filter	whether or not this dimer passed AlphaFold2 refolding interface confidence metrics	False

Citations

@article{varadi2021alphafold-f41, 
  year    = {2021}, 
  title   = {{AlphaFold} Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models}, 
  author  = {Varadi, Mihaly and Anyango, Stephen and Deshpande, Mandar and Nair, Sreenath and Natassia, Cindy and Yordanova, Galabina and Yuan, David and Stroe, Oana and Wood, Gemma and Laydon, Agata and Žídek, Augustin and Green, Tim and Tunyasuvunakool, Kathryn and Petersen, Stig and Jumper, John and Clancy, Ellen and Green, Richard and Vora, Ankur and Lutfi, Mira and Figurnov, Michael and Cowie, Andrew and Hobbs, Nicole and Kohli, Pushmeet and Kleywegt, Gerard and Birney, Ewan and Hassabis, Demis and Velankar, Sameer}, 
  journal = {Nucleic Acids Research}, 
  issn    = {0305-1048}, 
  doi     = {10.1093/nar/gkab1061}, 
  pmid    = {34791371}, 
  pmcid   = {{PMC}8728224}, 
  pages   = {D439--D444}, 
  number  = {D1}, 
  volume  = {50}
}
@article{lau2024exploring-e2f, 
  year    = {2024}, 
  title   = {Exploring structural diversity across the protein universe with The Encyclopedia of Domains}, 
  author  = {Lau, Andy M. and Bordin, Nicola and Kandathil, Shaun M. and Sillitoe, Ian and Waman, Vaishali P. and Wells, Jude and Orengo, Christine A. and Jones, David T.}, 
  journal = {Science}, 
  issn    = {0036-8075}, 
  doi     = {10.1126/science.adq4946}, 
  pmid    = {39480926}, 
  pages   = {eadq4946}, 
  number  = {6721}, 
  volume  = {386}
}
@article{kempen2022fast-33d, 
  year    = {2022}, 
  title   = {Fast and accurate protein structure search with Foldseek}, 
  author  = {Kempen, Michel van and Kim, Stephanie S and Tumescheit, Charlotte and Mirdita, Milot and Lee, Jeongjae and Gilchrist, Cameron L M and Söding, Johannes and Steinegger, Martin}, 
  journal = {{bioRxiv}}, 
  doi     = {10.1101/2022.02.07.479398}, 
  pages   = {2022.02.07.479398}
}
@article{jumper2021highly-969, 
  year    = {2021}, 
  title   = {Highly accurate protein structure prediction with {AlphaFold}}, 
  author  = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and Žídek, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A. A. and Ballard, Andrew J. and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W. and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis}, 
  journal = {Nature}, 
  issn    = {0028-0836}, 
  doi     = {10.1038/s41586-021-03819-2}, 
  pmid    = {34265844}, 
  pmcid   = {{PMC}8371605}, 
  pages   = {583--589}, 
  number  = {7873}, 
  volume  = {596}
}
@article{chaudhury2010pyrosetta-aec, 
  year    = {2010}, 
  title   = {{PyRosetta}: a script-based interface for implementing molecular modeling algorithms using Rosetta}, 
  author  = {Chaudhury, Sidhartha and Lyskov, Sergey and Gray, Jeffrey J.}, 
  journal = {Bioinformatics}, 
  issn    = {1367-4803}, 
  doi     = {10.1093/bioinformatics/btq007}, 
  pmid    = {20061306}, 
  pmcid   = {{PMC}2828115}, 
  pages   = {689--691}, 
  number  = {5}, 
  volume  = {26}
}