{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T09:37:01Z","timestamp":1781343421657,"version":"3.54.1"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2018,5,21]],"date-time":"2018-05-21T00:00:00Z","timestamp":1526860800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,2]]},"DOI":"10.1093\/nar\/gky427","type":"journal-article","created":{"date-parts":[[2018,5,7]],"date-time":"2018-05-07T19:14:31Z","timestamp":1525720471000},"page":"W296-W303","source":"Crossref","is-referenced-by-count":12124,"title":["SWISS-MODEL: homology modelling of protein structures and complexes"],"prefix":"10.1093","volume":"46","author":[{"given":"Andrew","family":"Waterhouse","sequence":"first","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martino","family":"Bertoni","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Bienert","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Studer","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerardo","family":"Tauriello","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafal","family":"Gumienny","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian T","family":"Heer","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tjaart A\u00a0P","family":"de\u00a0Beer","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Rempfer","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorenza","family":"Bordoli","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosalba","family":"Lepore","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2715-335X","authenticated-orcid":false,"given":"Torsten","family":"Schwede","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50\u201370, CH-4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,5,21]]},"reference":[{"key":"key\n\t\t\t\t20180630062751_B1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.drudis.2008.10.009","article-title":"Predicting druggable binding sites at the protein-protein interface","volume":"14","author":"Fuller","year":"2009","journal-title":"Drug Discov. Today"},{"key":"key\n\t\t\t\t20180630062751_B2","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1038\/nchembio.2026","article-title":"Pooled screening for antiproliferative inhibitors of protein-protein interactions","volume":"12","author":"Nim","year":"2016","journal-title":"Nat. Chem. Biol."},{"key":"key\n\t\t\t\t20180630062751_B3","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.str.2005.01.008","article-title":"Large macromolecular complexes in the Protein Data Bank: a status report","volume":"13","author":"Dutta","year":"2005","journal-title":"Structure"},{"key":"key\n\t\t\t\t20180630062751_B4","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1146\/annurev-biochem-060614-034142","article-title":"Structure, dynamics, assembly, and evolution of protein complexes","volume":"84","author":"Marsh","year":"2015","journal-title":"Annu. Rev. Biochem."},{"key":"key\n\t\t\t\t20180630062751_B5","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.sbi.2017.10.006","article-title":"The computational prediction of protein assemblies","volume":"46","author":"Tramontano","year":"2017","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20180630062751_B6","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1006\/jmbi.1997.1198","article-title":"Correlated mutations contain information about protein-protein interaction","volume":"271","author":"Pazos","year":"1997","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B7","doi-asserted-by":"crossref","first-page":"e03430","DOI":"10.7554\/eLife.03430","article-title":"Sequence co-evolution gives 3D contacts and structures of protein complexes","volume":"3","author":"Hopf","year":"2014","journal-title":"eLife"},{"key":"key\n\t\t\t\t20180630062751_B8","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1007\/978-1-59745-177-2_19","article-title":"Molecular docking","volume":"443","author":"Morris","year":"2008","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B9","doi-asserted-by":"crossref","first-page":"e22477","DOI":"10.1371\/journal.pone.0022477","article-title":"Benchmarking and analysis of protein docking performance in Rosetta v3.2","volume":"6","author":"Chaudhury","year":"2011","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180630062751_B10","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/s10822-017-0049-y","article-title":"Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2","volume":"32","author":"Kurkcuoglu","year":"2018","journal-title":"J. Computer-aided Mol. Des."},{"key":"key\n\t\t\t\t20180630062751_B11","doi-asserted-by":"crossref","first-page":"e1005937","DOI":"10.1371\/journal.pcbi.1005937","article-title":"Modeling the assembly order of multimeric heteroprotein complexes","volume":"14","author":"Peterson","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20180630062751_B12","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1110\/ps.041081905","article-title":"Assessing predictions of protein-protein interaction: the CAPRI experiment","volume":"14","author":"Janin","year":"2005","journal-title":"Protein Sci."},{"key":"key\n\t\t\t\t20180630062751_B13","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1002\/prot.24375","article-title":"The targets of CAPRI rounds 20\u201327","volume":"81","author":"Janin","year":"2013","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630062751_B14","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1007\/978-1-4939-1465-4_18","article-title":"Information-driven structural modelling of protein-protein interactions","volume":"1215","author":"Rodrigues","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B15","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/978-1-4939-6798-8_8","article-title":"Information-driven, ensemble flexible peptide docking using HADDOCK","volume":"1561","author":"Geng","year":"2017","journal-title":"Methods Mol. Biol."},{"issue":"Suppl. 1","key":"key\n\t\t\t\t20180630062751_B16","first-page":"311","article-title":"Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions","volume":"86","author":"Peterson","year":"2017","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630062751_B17","doi-asserted-by":"crossref","first-page":"10896","DOI":"10.1073\/pnas.1005894107","article-title":"Protein interface conservation across structure space","volume":"107","author":"Zhang","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180630062751_B18","doi-asserted-by":"crossref","first-page":"9438","DOI":"10.1073\/pnas.1200678109","article-title":"Templates are available to model nearly all complexes of structurally characterized proteins","volume":"109","author":"Kundrotas","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180630062751_B19","doi-asserted-by":"crossref","first-page":"2120","DOI":"10.1101\/gr.205301","article-title":"Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or \u201cinterologs\u201d","volume":"11","author":"Matthews","year":"2001","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180630062751_B20","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":"key\n\t\t\t\t20180630062751_B21","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.sbi.2013.11.005","article-title":"Template-based structure modeling of protein-protein interactions","volume":"24","author":"Szilagyi","year":"2014","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20180630062751_B22","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1101\/gr.1774904","article-title":"Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs","volume":"14","author":"Yu","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180630062751_B23","doi-asserted-by":"crossref","first-page":"10480","DOI":"10.1038\/s41598-017-09654-8","article-title":"Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology","volume":"7","author":"Bertoni","year":"2017","journal-title":"Scientific Rep."},{"issue":"Suppl. 1","key":"key\n\t\t\t\t20180630062751_B24","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1002\/prot.25408","article-title":"Assessment of protein assembly prediction in CASP12","volume":"86","author":"Lafita","year":"2018","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630062751_B25","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1042\/bst0240274","article-title":"ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling","volume":"24","author":"Peitsch","year":"1996","journal-title":"Biochem. Soc. Trans."},{"key":"key\n\t\t\t\t20180630062751_B26","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"},{"key":"key\n\t\t\t\t20180630062751_B27","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1093\/nar\/gkg520","article-title":"SWISS-MODEL: an automated protein homology-modeling server","volume":"31","author":"Schwede","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B28","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1093\/bioinformatics\/bti770","article-title":"The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling","volume":"22","author":"Arnold","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062751_B29","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/978-1-61779-588-6_5","article-title":"Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal","volume":"857","author":"Bordoli","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B30","doi-asserted-by":"crossref","first-page":"W252","DOI":"10.1093\/nar\/gku340","article-title":"SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information","volume":"42","author":"Biasini","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B31","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/bioinformatics\/btq662","article-title":"Toward the estimation of the absolute quality of individual protein structure models","volume":"27","author":"Benkert","year":"2011","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"key\n\t\t\t\t20180630062751_B32","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1002\/prot.25431","article-title":"Continuous automated model evaluation (CAMEO) complementing the critical assessment of structure prediction in CASP12","volume":"86","author":"Haas","year":"2018","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630062751_B33","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The Protein Data Bank","volume":"58","author":"Berman","year":"2002","journal-title":"Acta Crystallogr. D, Biol. Crystallogr."},{"key":"key\n\t\t\t\t20180630062751_B34","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt, C.","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B35","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B36","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180630062751_B37","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nmeth.1818","article-title":"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment","volume":"9","author":"Remmert","year":"2011","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180630062751_B38","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1107\/S0907444913007051","article-title":"OpenStructure: an integrated software framework for computational structural biology","volume":"69","author":"Biasini","year":"2013","journal-title":"Acta Crystallogr. D, Biol. Crystallogr."},{"key":"key\n\t\t\t\t20180630062751_B39","doi-asserted-by":"crossref","first-page":"D313","DOI":"10.1093\/nar\/gkw1132","article-title":"The SWISS-MODEL Repository\u2014new features and functionality","volume":"45","author":"Bienert","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B40","doi-asserted-by":"crossref","first-page":"D292","DOI":"10.1093\/nar\/gkt940","article-title":"PDBsum additions","volume":"42","author":"de\u00a0Beer","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B41","doi-asserted-by":"crossref","first-page":"D385","DOI":"10.1093\/nar\/gkv1047","article-title":"PDBe: improved accessibility of macromolecular structure data from PDB and EMDB","volume":"44","author":"Velankar","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B42","doi-asserted-by":"crossref","first-page":"D289","DOI":"10.1093\/nar\/gkw1098","article-title":"CATH: an expanded resource to predict protein function through structure and sequence","volume":"45","author":"Dawson","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B43","doi-asserted-by":"crossref","first-page":"W270","DOI":"10.1093\/nar\/gkr366","article-title":"SwissDock, a protein-small molecule docking web service based on EADock DSS","volume":"39","author":"Grosdidier","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B44","doi-asserted-by":"crossref","first-page":"2771","DOI":"10.1038\/nprot.2014.189","article-title":"Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected]","volume":"9","author":"Marcatili","year":"2014","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t20180630062751_B45","doi-asserted-by":"crossref","first-page":"2733","DOI":"10.1093\/bioinformatics\/btu194","article-title":"Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies","volume":"30","author":"Messih","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062751_B46","doi-asserted-by":"crossref","first-page":"W17","DOI":"10.1093\/nar\/gkx334","article-title":"PIGSPro: prediction of immunoGlobulin structures v2","volume":"45","author":"Lepore","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B47","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1016\/0022-2836(87)90412-8","article-title":"Canonical structures for the hypervariable regions of immunoglobulins","volume":"196","author":"Chothia","year":"1987","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B48","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1006\/jmbi.1997.1442","article-title":"Conformations of the third hypervariable region in the VH domain of immunoglobulins","volume":"275","author":"Morea","year":"1998","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B49","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/S0022-2836(05)80102-0","article-title":"Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins","volume":"215","author":"Tramontano","year":"1990","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B50","doi-asserted-by":"crossref","first-page":"W576","DOI":"10.1093\/nar\/gkv402","article-title":"NGL Viewer: a web application for molecular visualization","volume":"43","author":"Rose","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B51","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","article-title":"Comparative protein modelling by satisfaction of spatial restraints","volume":"234","author":"Sali","year":"1993","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180630062751_B52","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1016\/j.str.2011.03.019","article-title":"A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions","volume":"19","author":"Shapovalov","year":"2011","journal-title":"Structure"},{"key":"key\n\t\t\t\t20180630062751_B53","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/11415770_32","article-title":"Rapid protein Side-Chain packing via tree decomposition","volume-title":"Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14\u201318, 2005. Proceedings","author":"Xu","year":"2005"},{"key":"key\n\t\t\t\t20180630062751_B54","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1002\/prot.22488","article-title":"Improved prediction of protein side-chain conformations with SCWRL4","volume":"77","author":"Krivov","year":"2009","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630062751_B55","doi-asserted-by":"crossref","first-page":"e1005659","DOI":"10.1371\/journal.pcbi.1005659","article-title":"OpenMM 7: rapid development of high performance algorithms for molecular dynamics","volume":"13","author":"Eastman","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20180630062751_B56","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1002\/jcc.20065","article-title":"Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations","volume":"25","author":"Mackerell","year":"2004","journal-title":"J. Comput. Chem."},{"key":"key\n\t\t\t\t20180630062751_B57","doi-asserted-by":"crossref","first-page":"2722","DOI":"10.1093\/bioinformatics\/btt473","article-title":"lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests","volume":"29","author":"Mariani","year":"2013","journal-title":"Bioinformatics"},{"issue":"Suppl. 8","key":"key\n\t\t\t\t20180630062751_B58","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1002\/prot.21662","article-title":"Assessment of CASP7 predictions in the high accuracy template-based modeling category","volume":"69","author":"Read","year":"2007","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630062751_B59","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btq066","article-title":"How significant is a protein structure similarity with TM-score = 0.5","volume":"26","author":"Xu","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062751_B60","doi-asserted-by":"crossref","first-page":"2990","DOI":"10.1073\/pnas.061411798","article-title":"Identification of protein oligomerization states by analysis of interface conservation","volume":"98","author":"Elcock","year":"2001","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180630062751_B61","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1093\/bioinformatics\/btm270","article-title":"Predicting functionally important residues from sequence conservation","volume":"23","author":"Capra","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062751_B62","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.str.2008.12.014","article-title":"Outcome of a workshop on applications of protein models in biomedical research","volume":"17","author":"Schwede","year":"2009","journal-title":"Structure"},{"key":"key\n\t\t\t\t20180630062751_B63","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkh468","article-title":"Protein structure prediction and analysis using the Robetta server","volume":"32","author":"Kim","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630062751_B64","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/btr350","article-title":"Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates","volume":"27","author":"Yang","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630062751_B65","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1038\/nprot.2012.085","article-title":"Template-based protein structure modeling using the RaptorX web server","volume":"7","author":"Kallberg","year":"2012","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t20180630062751_B66","doi-asserted-by":"crossref","first-page":"14501","DOI":"10.1021\/bi011224c","article-title":"Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues","volume":"40","author":"Aliverti","year":"2001","journal-title":"Biochemistry"},{"key":"key\n\t\t\t\t20180630062751_B67","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/84097","article-title":"Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP(+) reductase","volume":"8","author":"Kurisu","year":"2001","journal-title":"Nat. Struct. Biol."},{"key":"key\n\t\t\t\t20180630062751_B68","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s11120-016-0331-1","article-title":"Structural basis for the isotype-specific interactions of ferredoxin and ferredoxin: NADP(+) oxidoreductase: an evolutionary switch between photosynthetic and heterotrophic assimilation","volume":"134","author":"Shinohara","year":"2017","journal-title":"Photosynth. Res."},{"key":"key\n\t\t\t\t20180630062751_B69","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1107\/S0907444900010052","article-title":"Crystallographic studies of the interaction between the ferredoxin-NADP+ reductase and ferredoxin from the cyanobacterium Anabaena: looking for the elusive ferredoxin molecule","volume":"56","author":"Morales","year":"2000","journal-title":"Acta Crystallogr. D, Biol. Crystallogr."},{"key":"key\n\t\t\t\t20180630062751_B70","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1186\/1471-2105-13-334","article-title":"Protein interface classification by evolutionary analysis","volume":"13","author":"Duarte","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180630062751_B71","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1016\/j.bbrc.2013.04.033","article-title":"Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin-NADP+ reductase","volume":"434","author":"Kimata-Ariga","year":"2013","journal-title":"Biochem. Biophys. Res. Commun."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/W1\/W296\/25110428\/gky427.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,17]],"date-time":"2019-10-17T17:34:51Z","timestamp":1571333691000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/46\/W1\/W296\/5000024"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5,21]]},"references-count":71,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2018,5,21]]},"published-print":{"date-parts":[[2018,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky427","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,2]]},"published":{"date-parts":[[2018,5,21]]}}}