{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:16Z","timestamp":1772138056329,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2022,8,13]],"date-time":"2022-08-13T00:00:00Z","timestamp":1660348800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"From the French Agence Nationale de la Recherche","award":["ANR-21-CE17-0046"],"award-info":[{"award-number":["ANR-21-CE17-0046"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>With the recent advances in protein 3D structure prediction, protein interactions are becoming more central than ever before. Here, we address the problem of determining how proteins interact with one another. More specifically, we investigate the possibility of discriminating near-native protein complex conformations from incorrect ones by exploiting local environments around interfacial residues.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Deep Local Analysis (DLA)-Ranker is a deep learning framework applying 3D convolutions to a set of locally oriented cubes representing the protein interface. It explicitly considers the local geometry of the interfacial residues along with their neighboring atoms and the regions of the interface with different solvent accessibility. We assessed its performance on three docking benchmarks made of half a million acceptable and incorrect conformations. We show that DLA-Ranker successfully identifies near-native conformations from ensembles generated by molecular docking. It surpasses or competes with other deep learning-based scoring functions. We also showcase its usefulness to discover alternative interfaces.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>http:\/\/gitlab.lcqb.upmc.fr\/dla-ranker\/DLA-Ranker.git<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac551","type":"journal-article","created":{"date-parts":[[2022,8,13]],"date-time":"2022-08-13T13:57:00Z","timestamp":1660399020000},"page":"4505-4512","source":"Crossref","is-referenced-by-count":14,"title":["Deep Local Analysis evaluates protein docking conformations with locally oriented cubes"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0254-6595","authenticated-orcid":false,"given":"Yasser","family":"Mohseni Behbahani","sequence":"first","affiliation":[{"name":"Sorbonne Universit\u00e9, CNRS, IBPS, Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238 , Paris 75005, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5012-4621","authenticated-orcid":false,"given":"Simon","family":"Crouzet","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9, CNRS, IBPS, Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238 , Paris 75005, France"}]},{"given":"Elodie","family":"Laine","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9, CNRS, IBPS, Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238 , Paris 75005, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2098-5743","authenticated-orcid":false,"given":"Alessandra","family":"Carbone","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9, CNRS, IBPS, Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238 , Paris 75005, France"}]}],"member":"286","published-online":{"date-parts":[[2022,8,13]]},"reference":[{"key":"2023041408232313300_","first-page":"265","author":"Abadi","year":"2016"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1038\/s41467-022-28865-w","article-title":"Improved prediction of protein-protein interactions using AlphaFold2","volume":"13","author":"Bryant","year":"2022","journal-title":"Nat. Commun"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1002\/prot.25888","article-title":"Energy-based graph convolutional networks for scoring protein docking models","volume":"88","author":"Cao","year":"2020","journal-title":"Proteins"},{"key":"2023041408232313300_","author":"Cohen","year":"2016"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"e1007624","DOI":"10.1371\/journal.pcbi.1007624","article-title":"Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties","volume":"16","author":"Corsi","year":"2020","journal-title":"PLoS Comput. Biol"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1093\/bioinformatics\/btw756","article-title":"The PPI3D web server for searching, analyzing and modeling protein\u2013protein interactions in the context of 3D structures","volume":"33","author":"Dapk\u016bnas","year":"2017","journal-title":"Bioinformatics"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"2613","DOI":"10.1021\/acs.jcim.7b00360","article-title":"INTerface builder: a fast protein\u2013protein interface reconstruction tool","volume":"57","author":"Dequeker","year":"2017","journal-title":"J. Chem. Inf. Model"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1002\/prot.25757","article-title":"Decrypting protein surfaces by combining evolution, geometry, and molecular docking","volume":"87","author":"Dequeker","year":"2019","journal-title":"Proteins"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"e1009825","DOI":"10.1371\/journal.pcbi.1009825","article-title":"From complete cross-docking to partners identification and binding sites predictions","volume":"18","author":"Dequeker","year":"2022","journal-title":"PLoS Comput. Biol"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: a protein protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J. Am. Chem. Soc"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1002\/prot.26033","article-title":"Hierarchical, rotation-equivariant neural networks to select structural models of protein complexes","volume":"89","author":"Eismann","year":"2021","journal-title":"Proteins"},{"key":"2023041408232313300_","author":"Evans","year":"2021"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/j.jmb.2003.10.069","article-title":"Identification of protein\u2013protein interaction sites from docking energy landscapes","volume":"335","author":"Fern\u00e1ndez-Recio","year":"2004","journal-title":"J. Mol. Biol"},{"key":"2023041408232313300_","author":"Fuchs","year":"2020"},{"key":"2023041408232313300_","author":"Ghani","year":"2021"},{"key":"2023041408232313300_","author":"Hubbard","year":"1993"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"eabm4805","DOI":"10.1126\/science.abm4805","article-title":"Computed structures of core eukaryotic protein complexes","volume":"374","author":"Humphreys","year":"2021","journal-title":"Science"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server for protein\u2013protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat. Protoc"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1002\/pro.3295","article-title":"Dockground: a comprehensive data resource for modeling of protein complexes","volume":"27","author":"Kundrotas","year":"2018","journal-title":"Protein Sci"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1002\/prot.25506","article-title":"Hidden partners: using cross-docking calculations to predict binding sites for proteins with multiple interactions","volume":"86","author":"Lagarde","year":"2018","journal-title":"Proteins"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"e1004580","DOI":"10.1371\/journal.pcbi.1004580","article-title":"Local geometry and evolutionary conservation of protein surfaces reveal the multiple recognition patches in protein-protein interactions","volume":"11","author":"Laine","year":"2015","journal-title":"PLoS Comput. Biol"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1002\/prot.25206","article-title":"Protein social behavior makes a stronger signal for partner identification than surface geometry","volume":"85","author":"Laine","year":"2017","journal-title":"Proteins"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1002\/prot.21804","article-title":"Docking and scoring protein complexes: CAPRI 3rd edition","volume":"69","author":"Lensink","year":"2007","journal-title":"Proteins"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1002\/prot.25215","article-title":"Modeling protein\u2013protein and protein\u2013peptide complexes: CAPRI 6th edition","volume":"85","author":"Lensink","year":"2017","journal-title":"Proteins"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1002\/prot.25870","article-title":"Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition","volume":"88","author":"Lensink","year":"2020","journal-title":"Proteins"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1016\/j.jmb.2010.09.028","article-title":"A simple definition of structural regions in proteins and its use in analyzing interface evolution","volume":"403","author":"Levy","year":"2010","journal-title":"J. Mol. Biol"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"2634","DOI":"10.1093\/bioinformatics\/btn497","article-title":"Dockground protein\u2013protein docking decoy set","volume":"24","author":"Liu","year":"2008","journal-title":"Bioinformatics"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"e1003369","DOI":"10.1371\/journal.pcbi.1003369","article-title":"Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information","volume":"9","author":"Lopes","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1002\/prot.20560","article-title":"Protein\u2013protein docking benchmark 2.0: an update","volume":"60","author":"Mintseris","year":"2005","journal-title":"Proteins"},{"key":"2023041408232313300_","first-page":"679","volume-title":"Nat. Meth.,","author":"Mirdita","year":"2022"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1093\/bioinformatics\/btx584","article-title":"Protein\u2013protein interaction specificity is captured by contact preferences and interface composition","volume":"34","author":"Nadalin","year":"2018","journal-title":"Bioinformatics"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"2757","DOI":"10.1093\/bioinformatics\/bty160","article-title":"RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules","volume":"34","author":"Neveu","year":"2018","journal-title":"Bioinformatics"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"3313","DOI":"10.1093\/bioinformatics\/btz122","article-title":"Protein model quality assessment using 3D oriented convolutional neural networks","volume":"35","author":"Pag\u00e8s","year":"2019","journal-title":"Bioinformatics"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1016\/j.str.2018.04.006","article-title":"Local interaction signal analysis predicts protein-protein binding affinity","volume":"26","author":"Raucci","year":"2018","journal-title":"Structure"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"7068","DOI":"10.1038\/s41467-021-27396-0","article-title":"DeepRank: a deep learning framework for data mining 3D protein-protein interfaces","volume":"12","author":"Renaud","year":"2021","journal-title":"Nat. Commun"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"D236","DOI":"10.1093\/nar\/gkw1053","article-title":"JET2 viewer: a database of predicted multiple, possibly overlapping, protein\u2013protein interaction sites for PDB structures","volume":"45","author":"Ripoche","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"2398","DOI":"10.1093\/bioinformatics\/btq444","article-title":"Ultra-fast FFT protein docking on graphics processors","volume":"26","author":"Ritchie","year":"2010","journal-title":"Bioinformatics"},{"key":"2023041408232313300_","author":"R\u00e9au","year":"2021"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.jmb.2008.08.002","article-title":"Identification of protein interaction partners and protein\u2013protein interaction sites","volume":"382","author":"Sacquin-Mora","year":"2008","journal-title":"J. Mol. Biol"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"e0221347","DOI":"10.1371\/journal.pone.0221347","article-title":"Protein model accuracy estimation based on local structure quality assessment using 3D convolutional neural network","volume":"14","author":"Sato","year":"2019","journal-title":"PLoS One"},{"key":"2023041408232313300_","author":"Thomas","year":"2018"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1002\/prot.20573","article-title":"Development and testing of an automated approach to protein docking","volume":"60","author":"Tovchigrechko","year":"2005","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"2023041408232313300_","volume-title":"International Conference on Learning Representations","author":"Veli\u010dkovi\u0107","year":"2018"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"3031","DOI":"10.1016\/j.jmb.2015.07.016","article-title":"Updates to the integrated protein\u2013protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2","volume":"427","author":"Vreven","year":"2015","journal-title":"J. Mol. Biol"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"2113","DOI":"10.1093\/bioinformatics\/btz870","article-title":"Protein docking model evaluation by 3D deep convolutional neural networks","volume":"36","author":"Wang","year":"2020","journal-title":"Bioinformatics"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"647915","DOI":"10.3389\/fmolb.2021.647915","article-title":"Protein docking model evaluation by graph neural networks","volume":"8","author":"Wang","year":"2021","journal-title":"Front. Mol. Biosci"},{"key":"2023041408232313300_","volume-title":"Advances in Neural Information Processing Systems","author":"Weiler","year":"2018"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1110\/ps.0239303","article-title":"Protein\u2013protein docking with a reduced protein model accounting for side-chain flexibility","volume":"12","author":"Zacharias","year":"2003","journal-title":"Protein Sci"},{"key":"2023041408232313300_","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1093\/nar\/gki524","article-title":"TM-align: a protein structure alignment algorithm based on the TM-score","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac551\/45477464\/btac551.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/19\/4505\/49884740\/btac551.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/19\/4505\/49884740\/btac551.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,25]],"date-time":"2023-11-25T14:27:10Z","timestamp":1700922430000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/19\/4505\/6665900"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,8,13]]},"references-count":52,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2022,9,30]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac551","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.04.05.487134","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,10,1]]},"published":{"date-parts":[[2022,8,13]]}}}