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3 results for “AF2Complex”
Input features of E. coli proteome for predicting and modeling protein-protein interactions with AF2Complex
<p>Input features to be used with AF2Complex for predicting protein-protein interactions among ~4400 E. coli proteins. A pickled feature file was generated by the feature data pipeline of AF2Complex for each E. coli protein. To reduce storage size, we limited up to 10,000 MSA sequences and up to 10 structural templates from the Protein Data Bank. The cutoff date for sequence libraries and the Protein Data Bank releases used for feature generation is no later than 11-30-2021.</p> <ul> <li>ecoli_af2c_fea.txt -- A list of all E coli protein with pre-generated input features</li> <li>af2c_fea_ecoli_220331_msa10ktem10.tar -- Input features named after the UniProt ID of each proteins. Note that after untar the tarball, you may use the gzipped feature pickle files directly with AF2Complex w/o gunzip.</li> </ul>
Input features and benchmark data sets for protein complex prediction and E. coli proteome application by AF2Complex
<p>Benchmark data sets of AF2Complex, input features for application to E. coli proteome, and predicted structural models of E. coli Ccm I as described in</p> <p><strong>Predicting direct physical interactions in multimeric proteins with deep learning</strong></p> <p><em>Mu Gao, Davi Nakajima An, Jerry M. Parks, Jeffrey Skolnick</em></p> <ol> <li><a href="https://zenodo.org/api/files/087ae188-6f7a-4a71-a586-bbc7bdcc6843/af2complex_bench.tar.gz">af2complex_bench.tar.gz</a>: Benchmark data sets CP17, Dimer1193 and Oligomer562, including input features for AF2Complex/AF-Multimer, both paired and unpaired MSAs, as well as sequences, experimental structures, and results presented in the AF2Complex work (~90GB de-compressed size)</li> <li><a href="https://zenodo.org/api/files/087ae188-6f7a-4a71-a586-bbc7bdcc6843/ecoli_Ccm_I.tar.gz">ecoli_Ccm_I.tar.gz</a>: Computational models of the<em> E. coli</em> Ccm I system</li> <li><a href="https://zenodo.org/api/files/087ae188-6f7a-4a71-a586-bbc7bdcc6843/ecoli_set.tar.gz">ecoli_sets.tar.gz</a>: Lists of benchmark sets of positive and negative PPIs from <em>E. coli</em></li> <li><a href="https://zenodo.org/api/files/087ae188-6f7a-4a71-a586-bbc7bdcc6843/ecoli_af_fea.tar.gz">ecoli_af_fea.tar.gz: </a>Pre-generated input features of <em>E. coli</em> proteome for protein complex prediction and modeling by AF2Complex (4,429 proteins, ~800 GB de-compressed size). This data set can be used with AF2Complex to probe the interactions of any combinations among the 4,429 proteins of E. coli.</li> </ol> <p> </p>
Predicted protein-protein interactions of the human tyrosine kinase Lck by AF2Complex
<p>Structural models and Supplementary data described in the publication:</p> <p>Predicting protein interactions of the kinase Lck critical to T cell modulation</p> <p>Structure (Cell Press), 2024</p> <p>Reference Authors: Mu Gao and Jeffrey Skolnick</p> <p><br>screening_results -- Virtual PPI screening results of the protein kinase Lck (SH3-SH2 domains as the bait).<br>predicted structural models.zip -- Compressed structural models described in the publication.<br>af2c_input_features -- Input features used to predict protein complex models with AF2Complex. </p>
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