2021 EMDataResource Ligand Model Challenge Dataset
DOI10.5281/zenodo.10551958Zenodo10551958MaRDI QIDQ6719815FDOQ6719815
Dataset published at Zenodo repository.
Daipayan Sarkar, Wei-Chun Kao, Sumit Mittal, Kevin Cowtan, Martyn Winn, Karunakar R. Pothula, Dong Si, Sean Lin, Corey Hryc, Bohdan Schneider, Mateusz Olek, Andriy Kryshtafovych, Nabin Giri, Andrew Muenks, Matthew L Baker, Helen M Berman, Chenghua Shao, Daisuke Kihara, Emmi Pohjolainen, Alberto Perez, Sundeep C. Vedithi, Carola Hunte, Michael F Schmid, Paul Emsley, Lijun Lang, Tom L. Blundell, Sigrid Noreng, Tom Burnley, Garib N. Murshudov, Abishek Singharoy, Minglei Zhao, Gunnar F Schröder, Maxim Igaev, Dilip Kumar, Frank DiMaio, Pavel V Afonine, Christopher J Williams, Chris I. Williams, Paul Bond, Christopher N. Rowley, Wah Chiu, Rangana Warshamanage, Stephen K. Burley, Greg D Pintilie, Xiao Wang, Luisa U Schäfer, Genki Terashi, Reza Esmaeeli, Helmut Grubmüller, Alberto Gobbi, Alexis L. Rohou, Sai R. Maddhuri Venkata Subramaniya, Jiří Černý, Jianlin Cheng, Andrea Vaiana, Mrinal Shekhar, Venkat Abbaraju, Jane S Richardson, Nigel W. Moriarty, Andrzej Joachimiak, Soon Wen Hoh, Colin M Palmer, Michael Prisant, Christopher J. Schlicksup, Keitaro Yamashita, Randy Read, Elizabeth Sourial, Agnel P Joseph, Vincent B. Chen, Ying Yang, Oleg V. Sobolev, Jie Hou, Arup Mondal, Simone Weyand, Jacob Verburgt, Catherine L Lawson, Benjamin D. Sellers, Renzhi Cao, Arthur Campbell, Robert A. Nicholls, Grzegorz Chojnowski
Publication date: 1 February 2024
Copyright license: Creative Commons Attribution 4.0 International
This is the full dataset of the 2021 Cryo-EM Map-based Model Ligand Challenge sponsored by EMDataResource (www.emdataresource.org, challenges.emdataresource.org, model-compare.emdataresource.org). The Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: (1) E. coli beta-galactosidase with inhibitor, (2) SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and (3) SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. File Descriptions: 2021-EMDataResource-Ligand-Challenge-web.pdf: Archive of challenges website content describing the challenge including News, Overview, Goals, Model Evaluation, Timeline, Targets, How to Participate, QA, Advisory Committee, Ligand Images T010X.zip: Submitted model files for each target (mmCIF and PDB formats) used for analyses S1_Ligand_Challenge_Statistics_Submission_Form.pdf: Overall model statistics, model submission form guide S2_submission_metadata.xlsx: Complete set of metadata collected for each submitted model S3_ligandchallengescores.xlsx: Compiled set of scores for this challenge from the model-compare site. WrapUp_MeetingAgendaLigandChallenge.pdf: Agenda of the July 26-28 2021 wrap up meeting zoom_discussion_mc_results.mp4: July 14 Model-Compare site analysis live demo recording
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