{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T13:43:46Z","timestamp":1776087826229,"version":"3.50.1"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T00:00:00Z","timestamp":1558310400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Key R&D Program of China","award":["2016YFA0501701"],"award-info":[{"award-number":["2016YFA0501701"]}]},{"name":"National Key R&D Program of China","award":["2016YFB0201700"],"award-info":[{"award-number":["2016YFB0201700"]}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["21575128"],"award-info":[{"award-number":["21575128"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["81773632"],"award-info":[{"award-number":["81773632"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Protein\u2013protein interactions (PPIs) play an important role in the different functions of cells, but accurate prediction of the three-dimensional structures for PPIs is still a notoriously difficult task. In this study, HawkDock, a free and open accessed web server, was developed to predict and analyze the structures of PPIs. In the HawkDock server, the ATTRACT docking algorithm, the HawkRank scoring function developed in our group and the MM\/GBSA free energy decomposition analysis were seamlessly integrated into a multi-functional platform. The structures of PPIs were predicted by combining the ATTRACT docking and the HawkRank re-scoring, and the key residues for PPIs were highlighted by the MM\/GBSA free energy decomposition. The molecular visualization was supported by 3Dmol.js. For the structural modeling of PPIs, HawkDock could achieve a better performance than ZDOCK 3.0.2 in the benchmark testing. For the prediction of key residues, the important residues that play an essential role in PPIs could be identified in the top 10 residues for \u223c81.4% predicted models and \u223c95.4% crystal structures in the benchmark dataset. To sum up, the HawkDock server is a powerful tool to predict the binding structures and identify the key residues of PPIs. The HawkDock server is accessible free of charge at http:\/\/cadd.zju.edu.cn\/hawkdock\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz397","type":"journal-article","created":{"date-parts":[[2019,5,1]],"date-time":"2019-05-01T19:13:01Z","timestamp":1556737981000},"page":"W322-W330","source":"Crossref","is-referenced-by-count":580,"title":["HawkDock: a web server to predict and analyze the protein\u2013protein complex based on computational docking and MM\/GBSA"],"prefix":"10.1093","volume":"47","author":[{"given":"Gaoqi","family":"Weng","sequence":"first","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China"}]},{"given":"Ercheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China"}]},{"given":"Zhe","family":"Wang","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China"}]},{"given":"Hui","family":"Liu","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8069-0053","authenticated-orcid":false,"given":"Feng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China"}]},{"given":"Dan","family":"Li","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China"}]},{"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China"},{"name":"State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China"}]}],"member":"286","published-online":{"date-parts":[[2019,5,20]]},"reference":[{"key":"2019062808224047800_B1","doi-asserted-by":"crossref","first-page":"e380","DOI":"10.1038\/oncsis.2017.79","article-title":"Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes","volume":"6","author":"Gress","year":"2017","journal-title":"Oncogenesis"},{"key":"2019062808224047800_B2","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1016\/j.bpj.2014.08.033","article-title":"Protein-protein docking: from interaction to interactome","volume":"107","author":"Vakser","year":"2014","journal-title":"Biophys. J."},{"key":"2019062808224047800_B3","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/bib\/bbt047","article-title":"Evaluating template-based and template-free protein\u2013protein complex structure prediction","volume":"15","author":"Vreven","year":"2014","journal-title":"Brief. Bioinform."},{"key":"2019062808224047800_B4","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1016\/j.jmb.2003.07.006","article-title":"The relationship between sequence and interaction divergence in proteins","volume":"332","author":"Aloy","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2019062808224047800_B5","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.bpj.2014.12.015","article-title":"A web interface for easy flexible protein\u2013protein docking with ATTRACT","volume":"108","author":"de\u00a0Vries","year":"2015","journal-title":"Biophys. J."},{"key":"2019062808224047800_B6","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":"2019062808224047800_B7","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1038\/nprot.2010.32","article-title":"The HADDOCK web server for data-driven biomolecular docking","volume":"5","author":"de\u00a0Vries","year":"2010","journal-title":"Nat. Protoc."},{"key":"2019062808224047800_B8","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1093\/bioinformatics\/btu097","article-title":"ZDOCK server: interactive docking prediction of protein\u2013protein complexes and symmetric multimers","volume":"30","author":"Pierce","year":"2014","journal-title":"Bioinformatics"},{"key":"2019062808224047800_B9","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1093\/bioinformatics\/btt038","article-title":"SwarmDock: a server for flexible protein\u2013protein docking","volume":"29","author":"Torchala","year":"2013","journal-title":"Bioinformatics"},{"key":"2019062808224047800_B10","doi-asserted-by":"crossref","first-page":"W356","DOI":"10.1093\/nar\/gkv368","article-title":"pyDockSAXS: protein\u2013protein complex structure by SAXS and computational docking","volume":"43","author":"Jimenez-Garcia","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B11","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1093\/bioinformatics\/btt262","article-title":"pyDockWEB: a web server for rigid-body protein\u2013protein docking using electrostatics and desolvation scoring","volume":"29","author":"Jimenez-Garcia","year":"2013","journal-title":"Bioinformatics"},{"key":"2019062808224047800_B12","doi-asserted-by":"crossref","first-page":"W408","DOI":"10.1093\/nar\/gky377","article-title":"InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs","volume":"46","author":"Quignot","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B13","doi-asserted-by":"crossref","first-page":"W310","DOI":"10.1093\/nar\/gkl206","article-title":"GRAMM-X public web server for protein\u2013protein docking","volume":"34","author":"Tovchigrechko","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B14","doi-asserted-by":"crossref","first-page":"W233","DOI":"10.1093\/nar\/gkn216","article-title":"The RosettaDock server for local protein\u2013protein docking","volume":"36","author":"Lyskov","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B15","doi-asserted-by":"crossref","first-page":"W363","DOI":"10.1093\/nar\/gki481","article-title":"PatchDock and SymmDock: servers for rigid and symmetric docking","volume":"33","author":"Schneidman-Duhovny","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B16","doi-asserted-by":"crossref","first-page":"W445","DOI":"10.1093\/nar\/gkq311","article-title":"HexServer: an FFT-based protein docking server powered by graphics processors","volume":"38","author":"Macindoe","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B17","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1093\/bioinformatics\/btn093","article-title":"3D-Garden: a system for modelling protein\u2013protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm","volume":"24","author":"Lesk","year":"2008","journal-title":"Bioinformatics"},{"key":"2019062808224047800_B18","doi-asserted-by":"crossref","first-page":"2386","DOI":"10.1093\/bioinformatics\/btw141","article-title":"FRODOCK 2.0: fast protein\u2013protein docking server","volume":"32","author":"Ramirez-Aportela","year":"2016","journal-title":"Bioinformatics"},{"key":"2019062808224047800_B19","doi-asserted-by":"crossref","first-page":"W365","DOI":"10.1093\/nar\/gkx407","article-title":"HDOCK: a web server for protein\u2013protein and protein-DNA\/RNA docking based on a hybrid strategy","volume":"45","author":"Yan","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B20","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1126\/science.7529940","article-title":"A hot spot of binding energy in a hormone-receptor interface","volume":"267","author":"Clackson","year":"1995","journal-title":"Science"},{"key":"2019062808224047800_B21","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1002\/jcc.10379","article-title":"Converging free energy estimates: MM-PB(GB)SA studies on the protein\u2013protein complex Ras-Raf","volume":"25","author":"Gohlke","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2019062808224047800_B22","doi-asserted-by":"crossref","first-page":"2626","DOI":"10.1021\/ci4002475","article-title":"MMGBSA as a tool to understand the binding affinities of filamin-peptide interactions","volume":"53","author":"Ylilauri","year":"2013","journal-title":"J. Chem. Inf. Model."},{"key":"2019062808224047800_B23","doi-asserted-by":"crossref","first-page":"e1004313","DOI":"10.1371\/journal.pcbi.1004313","article-title":"Detailed per-residue energetic analysis explains the driving force for microtubule disassembly","volume":"11","author":"Ayoub","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"2019062808224047800_B24","doi-asserted-by":"crossref","first-page":"2250","DOI":"10.1021\/acs.jcim.7b00181","article-title":"A computational investigation of small-molecule engagement of hot spots at protein\u2013protein interaction interfaces","volume":"57","author":"Xu","year":"2017","journal-title":"J. Chem. Inf. Model."},{"key":"2019062808224047800_B25","doi-asserted-by":"crossref","first-page":"22129","DOI":"10.1039\/C6CP03670H","article-title":"Assessing the performance of the MM\/PBSA and MM\/GBSA methods. 6. Capability to predict protein\u2013protein binding free energies and re-rank binding poses generated by protein\u2013protein docking","volume":"18","author":"Chen","year":"2016","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2019062808224047800_B26","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1371\/journal.pcbi.0020001","article-title":"Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain","volume":"2","author":"Hou","year":"2006","journal-title":"PLoS Comput. Biol."},{"key":"2019062808224047800_B27","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1093\/bioinformatics\/btr294","article-title":"Prediction of peptides binding to the PKA RII\u03b1 subunit using a hierarchical strategy","volume":"27","author":"Hou","year":"2011","journal-title":"Bioinformatics"},{"key":"2019062808224047800_B28","doi-asserted-by":"crossref","first-page":"2982","DOI":"10.1021\/pr3000688","article-title":"Characterization of domain-peptide interaction interface: Prediction of SH3 domain-mediated protein\u2013protein interaction network in yeast by generic structure-based models","volume":"11","author":"Hou","year":"2012","journal-title":"J. Proteome Res."},{"key":"2019062808224047800_B29","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1002\/jcc.25592","article-title":"Calculation of hot spots for protein\u2013protein interaction in p53\/PMI\u2010MDM2\/MDMX complexes","volume":"40","author":"Huang","year":"2019","journal-title":"J. Comput. Chem."},{"key":"2019062808224047800_B30","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1002\/pro.2027","article-title":"Prediction of protein\u2013protein binding free energies","volume":"21","author":"Vreven","year":"2012","journal-title":"Protein Sci."},{"key":"2019062808224047800_B31","doi-asserted-by":"crossref","first-page":"e1004981","DOI":"10.1371\/journal.pcbi.1004981","article-title":"Deciphering dimerization modes of PAS Domains: Computational and experimental analyses of the AhR:ARNT complex reveal new insights into the mechanisms of AhR transformation","volume":"12","author":"Corrada","year":"2016","journal-title":"PLoS Comput. Biol."},{"key":"2019062808224047800_B32","doi-asserted-by":"crossref","first-page":"2823","DOI":"10.1039\/C4CP04544K","article-title":"Energetic contributions of residues to the formation of early amyloid-beta oligomers","volume":"17","author":"Pouplana","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2019062808224047800_B33","doi-asserted-by":"crossref","first-page":"3370","DOI":"10.1039\/C4CP05095A","article-title":"Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches","volume":"17","author":"Xu","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2019062808224047800_B34","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13321-017-0254-7","article-title":"HawkRank: a new scoring function for protein\u2013protein docking based on weighted energy terms","volume":"9","author":"Feng","year":"2017","journal-title":"J. Cheminform."},{"key":"2019062808224047800_B35","doi-asserted-by":"crossref","first-page":"11295","DOI":"10.1021\/jp025595u","article-title":"Empirical aqueous solvation models based on accessible surface areas with implicit electrostatics","volume":"106","author":"Hou","year":"2002","journal-title":"J. Phys. Chem. B"},{"key":"2019062808224047800_B36","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1110\/ps.0239303","article-title":"Protein-protein docking with a reduced protein model accounting for side-chain flexibility","volume":"12","author":"Zacharias","year":"2003","journal-title":"Protein Sci."},{"key":"2019062808224047800_B37","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1093\/bioinformatics\/btu829","article-title":"3Dmol.js: molecular visualization with WebGL","volume":"31","author":"Rego","year":"2015","journal-title":"Bioinformatics"},{"key":"2019062808224047800_B38","doi-asserted-by":"crossref","first-page":"1810","DOI":"10.1002\/prot.24078","article-title":"Clustering biomolecular complexes by residue contacts similarity","volume":"80","author":"Rodrigues","year":"2012","journal-title":"Proteins"},{"key":"2019062808224047800_B39","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1002\/jcc.1065","article-title":"Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform\/water partition coefficients of the nucleic acid bases","volume":"22","author":"Cieplak","year":"2001","journal-title":"J. Comput. Chem."},{"key":"2019062808224047800_B40","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1002\/prot.20033","article-title":"Exploring protein native states and large-scale conformational changes with a modified generalized born model","volume":"55","author":"Onufriev","year":"2004","journal-title":"Proteins"},{"key":"2019062808224047800_B41","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J. Comput. Chem."},{"key":"2019062808224047800_B42","doi-asserted-by":"crossref","first-page":"W665","DOI":"10.1093\/nar\/gkh381","article-title":"PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations","volume":"32","author":"Dolinsky","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2019062808224047800_B43","doi-asserted-by":"crossref","first-page":"3111","DOI":"10.1002\/prot.22830","article-title":"Protein-protein docking benchmark version 4.0","volume":"78","author":"Hwang","year":"2010","journal-title":"Proteins"},{"key":"2019062808224047800_B44","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1002\/prot.10381","article-title":"CAPRI: A critical assessment of predicted interactions","volume":"52","author":"Janin","year":"2003","journal-title":"Proteins"},{"key":"2019062808224047800_B45","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1186\/1471-2105-10-407","article-title":"Protein-protein docking using region-based 3D Zernike descriptors","volume":"10","author":"Venkatraman","year":"2009","journal-title":"BMC Bioinform"},{"key":"2019062808224047800_B46","doi-asserted-by":"crossref","first-page":"e24657","DOI":"10.1371\/journal.pone.0024657","article-title":"Accelerating protein docking in ZDOCK using an advanced 3D convolution library","volume":"6","author":"Pierce","year":"2011","journal-title":"PLoS One"},{"key":"2019062808224047800_B47","doi-asserted-by":"crossref","first-page":"1894","DOI":"10.1110\/ps.036624.108","article-title":"Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d","volume":"17","author":"Haspel","year":"2008","journal-title":"Protein Sci."},{"key":"2019062808224047800_B48","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1126\/science.280.5367.1277","article-title":"X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2","volume":"280","author":"Nagar","year":"1998","journal-title":"Science"},{"key":"2019062808224047800_B49","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/ni1450","article-title":"A structural basis for complement inhibition by Staphylococcus aureus","volume":"8","author":"Hammel","year":"2007","journal-title":"Nat. Immunol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz397\/28672441\/gkz397.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/W1\/W322\/28879901\/gkz397.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T14:31:00Z","timestamp":1721226660000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/W1\/W322\/5491747"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,20]]},"references-count":49,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2019,5,20]]},"published-print":{"date-parts":[[2019,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz397","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7,2]]},"published":{"date-parts":[[2019,5,20]]}}}