{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T04:47:08Z","timestamp":1778647628865,"version":"3.51.4"},"reference-count":97,"publisher":"Oxford University Press (OUP)","issue":"6","funder":[{"DOI":"10.13039\/100006952","name":"Louisiana Board of Regents through the Board of Regents Support Fund","doi-asserted-by":"publisher","award":["LEQSF(2012-15)-RD-A-05"],"award-info":[{"award-number":["LEQSF(2012-15)-RD-A-05"]}],"id":[{"id":"10.13039\/100006952","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>It has been more than a decade since the completion of the Human Genome Project that provided us with a complete list of human proteins. The next obvious task is to figure out how various parts interact with each other. On that account, we review 10 methods for protein interface prediction, which are freely available as web servers. In addition, we comparatively evaluate their performance on a common data set comprising different quality target structures. We find that using experimental structures and high-quality homology models, structure-based methods outperform those using only protein sequences, with global template-based approaches providing the best performance. For moderate-quality models, sequence-based methods often perform better than those structure-based techniques that rely on fine atomic details. We note that post-processing protocols implemented in several methods quantitatively improve the results only for experimental structures, suggesting that these procedures should be tuned up for computer-generated models. Finally, we anticipate that advanced meta-prediction protocols are likely to enhance interface residue prediction. Notwithstanding further improvements, easily accessible web servers already provide the scientific community with convenient resources for the identification of protein\u2013protein interaction sites.<\/jats:p>","DOI":"10.1093\/bib\/bbv009","type":"journal-article","created":{"date-parts":[[2015,3,23]],"date-time":"2015-03-23T00:02:32Z","timestamp":1427068952000},"page":"1025-1034","source":"Crossref","is-referenced-by-count":42,"title":["Predicting protein interface residues using easily accessible on-line resources"],"prefix":"10.1093","volume":"16","author":[{"given":"Surabhi","family":"Maheshwari","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michal","family":"Brylinski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,3,21]]},"reference":[{"key":"2019062808523101700_bbv009-B1","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/nature04209","article-title":"Towards a proteome-scale map of the human protein-protein interaction network","volume":"437","author":"Rual","year":"2005","journal-title":"Nature"},{"key":"2019062808523101700_bbv009-B2","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/nature06526","article-title":"Reaching for high-hanging fruit in drug discovery at protein-protein interfaces","volume":"450","author":"Wells","year":"2007","journal-title":"Nature"},{"key":"2019062808523101700_bbv009-B3","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.tips.2012.03.006","article-title":"Structural biology and drug discovery for protein\u2013protein interactions","volume":"33","author":"Jubb","year":"2012","journal-title":"Trends Pharmacol Sci"},{"key":"2019062808523101700_bbv009-B4","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1073\/pnas.030409597","article-title":"A regulator of G protein signaling interaction surface linked to effector specificity","volume":"97","author":"Sowa","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019062808523101700_bbv009-B5","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1038\/84974","article-title":"Prediction and confirmation of a site critical for effector regulation of RGS domain activity","volume":"8","author":"Sowa","year":"2001","journal-title":"Nat Struct Biol"},{"key":"2019062808523101700_bbv009-B6","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1002\/prot.10115","article-title":"Principles of docking: an overview of search algorithms and a guide to scoring functions","volume":"47","author":"Halperin","year":"2002","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B7","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1016\/j.jmb.2006.01.001","article-title":"Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment","volume":"357","author":"Chelliah","year":"2006","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B8","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-13-7","article-title":"Protein docking prediction using predicted protein-protein interface","volume":"13","author":"Li","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2019062808523101700_bbv009-B9","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1038\/13732","article-title":"A generic protein purification method for protein complex characterization and proteome exploration","volume":"17","author":"Rigaut","year":"1999","journal-title":"Nat Biotechnol"},{"key":"2019062808523101700_bbv009-B10","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/S0959-440X(02)00400-1","article-title":"Protein complexes gain momentum","volume":"12","author":"Sobott","year":"2002","journal-title":"Curr Opin Struct Biol"},{"key":"2019062808523101700_bbv009-B11","first-page":"5","article-title":"Mass spectrometry from genomics to proteomics","volume":"16","author":"Yates","year":"2000","journal-title":"Outlook"},{"key":"2019062808523101700_bbv009-B12","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","article-title":"Assigning protein functions by comparative genome analysis: protein phylogenetic profiles","volume":"96","author":"Pellegrini","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019062808523101700_bbv009-B13","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/S0955-0674(03)00009-7","article-title":"Function prediction and protein networks","volume":"15","author":"Huynen","year":"2003","journal-title":"Curr. Opin. Cell Biol."},{"key":"2019062808523101700_bbv009-B14","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1002\/prot.10074","article-title":"In silico two-hybrid system for the selection of physically interacting protein pairs","volume":"47","author":"Pazos","year":"2002","journal-title":"Proteins Struct Funct Genet"},{"key":"2019062808523101700_bbv009-B15","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1006\/jmbi.1997.1233","article-title":"Prediction of protein-protein interaction sites using patch analysis","volume":"272","author":"Jones","year":"1997","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B16","first-page":"445","article-title":"Computational prediction of protein-protein interactions","volume":"261","author":"Obenauer","year":"2004","journal-title":"Methods Mol Biol"},{"key":"2019062808523101700_bbv009-B17","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1002\/prot.21248","article-title":"Prediction-based fingerprints of protein \u2013 protein interactions","volume":"645","author":"Porollo","year":"2007","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B18","first-page":"247","article-title":"Computational methods for predicting protein-protein interactions","volume":"110","author":"Pitre","year":"2008","journal-title":"Adv Biochem Eng Biotechnol"},{"key":"2019062808523101700_bbv009-B19","doi-asserted-by":"crossref","first-page":"177","DOI":"10.2174\/1574893611308020005","article-title":"Current status of machine learning-based methods for identifying protein-protein interaction sites","volume":"8","author":"Wang","year":"2013","journal-title":"Curr Bioinform"},{"key":"2019062808523101700_bbv009-B20","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/S0014-5793(03)00456-3","article-title":"Predicted protein-protein interaction sites from local sequence information","volume":"544","author":"Ofran","year":"2003","journal-title":"FEBS Lett"},{"key":"2019062808523101700_bbv009-B21","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1006\/jmbi.1996.0167","article-title":"An evolutionary trace method defines binding surfaces common to protein families","volume":"257","author":"Lichtarge","year":"1996","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B22","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/bioinformatics\/btp039","article-title":"Sequence-based prediction of protein interaction sites with an integrative method","volume":"25","author":"Chen","year":"2009","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B23","doi-asserted-by":"crossref","first-page":"e1000278","DOI":"10.1371\/journal.pcbi.1000278","article-title":"Prediction of protein-protein interaction sites in sequences and 3D structures by random forests","volume":"5","author":"Siki\u0107","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2019062808523101700_bbv009-B24","doi-asserted-by":"crossref","first-page":"2203","DOI":"10.1093\/bioinformatics\/btm323","article-title":"Interaction-site prediction for protein complexes: a critical assessment","volume":"23","author":"Zhou","year":"2007","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B25","doi-asserted-by":"crossref","first-page":"394","DOI":"10.2174\/138920308785132712","article-title":"How proteins get in touch: interface prediction in the study of bio- molecular complexes","volume":"9","author":"de Vries","year":"2008","journal-title":"Curr Protein Pept Sci"},{"key":"2019062808523101700_bbv009-B26","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1093\/bib\/bbp021","article-title":"Progress and challenges in predicting protein-protein interaction sites","volume":"10","author":"Ezkurdia","year":"2009","journal-title":"Brief Bioinform"},{"key":"2019062808523101700_bbv009-B27","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1110\/ps.03323604","article-title":"Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?","volume":"13","author":"Caffrey","year":"2004","journal-title":"Protein Sci"},{"key":"2019062808523101700_bbv009-B28","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1002\/prot.21233","article-title":"PIER: protein interface recognition for structural proteomics","volume":"417","author":"Kufareva","year":"2007","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B29","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1093\/bioinformatics\/btl303","article-title":"ISIS: interaction sites identified from sequence","volume":"23","author":"Ofran","year":"2007","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B30","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1002\/prot.20433","article-title":"Statistical analysis and prediction of protein-protein interfaces","volume":"60","author":"Bordner","year":"2005","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B31","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1002\/jmr.2410","article-title":"Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning","volume":"28","author":"Maheshwari","year":"2015","journal-title":"J Mol Recognit"},{"key":"2019062808523101700_bbv009-B32","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/prot.20514","article-title":"Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data","volume":"61","author":"Chen","year":"2005","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B33","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1006\/jmbi.1997.1234","article-title":"Analysis of protein-protein interaction sites using surface patches","volume":"272","author":"Jones","year":"1997","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B34","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1073\/pnas.93.1.13","article-title":"Review Principles of protein-protein interactions","volume":"93","author":"Jones","year":"1996","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019062808523101700_bbv009-B35","doi-asserted-by":"crossref","first-page":"1921","DOI":"10.1016\/j.bpj.2009.12.4332","article-title":"Prediction of protein-protein interaction sites using electrostatic desolvation profiles","volume":"98","author":"Fiorucci","year":"2010","journal-title":"Biophys J"},{"key":"2019062808523101700_bbv009-B36","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/btq302","article-title":"Applying the Na\u00efve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites","volume":"26","author":"Murakami","year":"2010","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B37","doi-asserted-by":"crossref","first-page":"3397","DOI":"10.1093\/bioinformatics\/btm474","article-title":"InterProSurf: a web server for predicting interacting sites on protein surfaces","volume":"23","author":"Negi","year":"2007","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B38","doi-asserted-by":"crossref","first-page":"3698","DOI":"10.1093\/nar\/gkl454","article-title":"Protein binding site prediction using an empirical scoring function","volume":"34","author":"Liang","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2019062808523101700_bbv009-B39","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.jmb.2004.02.040","article-title":"ProMate: a structure based prediction program to identify the location of protein-protein binding sites","volume":"338","author":"Neuvirth","year":"2004","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B40","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1186\/1471-2105-12-352","article-title":"Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi Diagrams","volume":"12","author":"Segura","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2019062808523101700_bbv009-B41","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-13-41","article-title":"Predicting protein-protein interface residues using local surface structural similarity","volume":"13","author":"Jordan","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2019062808523101700_bbv009-B42","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1088\/1478-3975\/2\/2\/S01","article-title":"Prediction of physical protein \u2013 protein interactions","volume":"2","author":"Grimm","year":"2005","journal-title":"Phys Biol"},{"key":"2019062808523101700_bbv009-B43","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.ijbiomac.2006.02.024","article-title":"Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores","volume":"38","author":"Li","year":"2006","journal-title":"Int J Biol Macromol"},{"key":"2019062808523101700_bbv009-B44","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1016\/j.febslet.2005.11.081","article-title":"Predicting protein interaction sites from residue spatial sequence profile and evolution rate","volume":"580","author":"Wang","year":"2006","journal-title":"FEBS Lett"},{"key":"2019062808523101700_bbv009-B45","doi-asserted-by":"crossref","first-page":"999","DOI":"10.2174\/092986606778777498","article-title":"Inferring protein-protein interacting sites using residue conservation and evolutionary information","volume":"13","author":"Wang","year":"2006","journal-title":"Protein Pept Lett"},{"key":"2019062808523101700_bbv009-B46","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1002\/prot.20842","article-title":"WHISCY: what information does surface conservation yield? Application to Data-Driven Docking","volume":"489","author":"de Vries","year":"2006","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B47","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1002\/prot.1099","article-title":"Prediction of protein interaction sites from sequence profile and residue neighbor list","volume":"44","author":"Zhou","year":"2001","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B48","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1093\/protein\/gzh020","article-title":"Prediction of protein-protein interaction sites using support vector machines","volume":"17","author":"Koike","year":"2004","journal-title":"Protein Eng Des Sel"},{"key":"2019062808523101700_bbv009-B49","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 USA"},{"key":"2019062808523101700_bbv009-B50","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1006\/jmbi.2000.4474","article-title":"ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information","volume":"307","author":"Armon","year":"2001","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B51","doi-asserted-by":"crossref","first-page":"1444","DOI":"10.1002\/prot.24512","article-title":"Benchmarking protein-protein interface predictions: why you should care about protein size","volume":"82","author":"Martin","year":"2014","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B52","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/S1093-3263(00)00138-8","article-title":"Intrinsically disordered protein","volume":"19","author":"Dunker","year":"2001","journal-title":"J Mol Graph Model"},{"key":"2019062808523101700_bbv009-B53","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1002\/pro.2207","article-title":"Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding","volume":"22","author":"Hsu","year":"2013","journal-title":"Protein Sci"},{"key":"2019062808523101700_bbv009-B54","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1002\/prot.21281","article-title":"Role of intrinsic disorder in transient interactions of hub proteins","volume":"66","author":"Singh","year":"2007","journal-title":"Proteins Struct Funct Genet"},{"key":"2019062808523101700_bbv009-B55","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1016\/j.jmb.2006.07.087","article-title":"Analysis of molecular recognition features (MoRFs)","volume":"362","author":"Mohan","year":"2006","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B56","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.jmb.2011.10.025","article-title":"Prediction of short linear protein binding regions","volume":"415","author":"Mooney","year":"2012","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B57","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/bioinformatics\/bts209","article-title":"MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins","volume":"28","author":"Disfani","year":"2012","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B58","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1093\/bioinformatics\/btp518","article-title":"ANCHOR: web server for predicting protein binding regions in disordered proteins","volume":"25","author":"Doszt\u00e1nyi","year":"2009","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B59","doi-asserted-by":"crossref","first-page":"6806","DOI":"10.1021\/cr4007329","article-title":"Disordered proteinaceous machines","volume":"114","author":"Fuxreiter","year":"2014","journal-title":"Chem Rev"},{"key":"2019062808523101700_bbv009-B60","doi-asserted-by":"crossref","first-page":"W283","DOI":"10.1093\/nar\/gkr311","article-title":"PredUs: a web server for predicting protein interfaces using structural neighbors","volume":"39","author":"Zhang","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2019062808523101700_bbv009-B61","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":"2019062808523101700_bbv009-B62","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"2019062808523101700_bbv009-B63","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1089\/cmb.2005.12.355","article-title":"Linear regression models for solvent accessibility prediction in proteins","volume":"12","author":"Wagner","year":"2005","journal-title":"J Comput Biol"},{"key":"2019062808523101700_bbv009-B64","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1002\/prot.22106","article-title":"Protein-protein docking benchmark version 3.0","volume":"73","author":"Hwang","year":"2009","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B65","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1007\/s00894-007-0237-0","article-title":"Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces","volume":"13","author":"Negi","year":"2007","journal-title":"J Mol Model"},{"key":"2019062808523101700_bbv009-B66","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1002\/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.0.CO;2-W","article-title":"Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules","volume":"19","author":"Fraczkiewicz","year":"1998","journal-title":"J Comput Chem"},{"key":"2019062808523101700_bbv009-B67","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1093\/bioinformatics\/17.8.700","article-title":"AL2CO: calculation of positional conservation in a protein sequence alignment","volume":"17","author":"Pei","year":"2001","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B68","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1002\/prot.340090107","article-title":"Database of homology-derived protein structures and the structural meaning of sequence alignment","volume":"9","author":"Sander","year":"1991","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B69","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 Vries","year":"2010","journal-title":"Nat Protoc"},{"key":"2019062808523101700_bbv009-B70","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1002\/prot.10390","article-title":"A protein-protein docking benchmark","volume":"52","author":"Chen","year":"2003","journal-title":"Proteins Struct Funct Genet"},{"key":"2019062808523101700_bbv009-B71","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1002\/prot.20285","article-title":"Optimal docking area: a new method for predicting protein-protein interaction sites","volume":"58","author":"Fernandez-Recio","year":"2005","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B72","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1002\/jcc.540150503","article-title":"ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation","volume":"15","author":"Abagyan","year":"1994","journal-title":"J Comput Chem"},{"key":"2019062808523101700_bbv009-B73","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1006\/jmbi.1997.1287","article-title":"Do aligned sequences share the same fold?","volume":"273","author":"Abagyan","year":"1997","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B74","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1126\/science.6879170","article-title":"Solvent-accessible surfaces of proteins and nucleic acids","volume":"221","author":"Connolly","year":"1983","journal-title":"Science"},{"key":"2019062808523101700_bbv009-B75","doi-asserted-by":"crossref","first-page":"e50200","DOI":"10.1371\/journal.pone.0050200","article-title":"eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures","volume":"7","author":"Brylinski","year":"2012","journal-title":"PLoS One"},{"key":"2019062808523101700_bbv009-B76","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1186\/1471-2105-9-531","article-title":"Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score","volume":"9","author":"Pandit","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2019062808523101700_bbv009-B77","first-page":"3","article-title":"The optimality of naive bayes","volume":"1","author":"Zhang","year":"2004","journal-title":"Mach Learn"},{"key":"2019062808523101700_bbv009-B78","doi-asserted-by":"crossref","first-page":"e1000267","DOI":"10.1371\/journal.pcbi.1000267","article-title":"Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling","volume":"5","author":"Engelen","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2019062808523101700_bbv009-B79","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1006\/jmbi.2000.3973","article-title":"An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance","volume":"301","author":"Yang","year":"2000","journal-title":"J Mol Biol"},{"key":"2019062808523101700_bbv009-B80","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/S0968-0004(98)01253-5","article-title":"PQS: a protein quaternary structure file server","volume":"23","author":"Henrick","year":"1998","journal-title":"Trends Biochem Sci"},{"key":"2019062808523101700_bbv009-B81","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":"2019062808523101700_bbv009-B82","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1002\/prot.340110407","article-title":"Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons","volume":"11","author":"Nicholls","year":"1991","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B83","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/1961189.1961199","article-title":"LIBSVM: a library for support vector machines","volume":"2","author":"Chang","year":"2011","journal-title":"ACM Trans Intell Syst Technol"},{"key":"2019062808523101700_bbv009-B84","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1021\/cr040409x","article-title":"Principles of protein-protein interactions: what are the preferred ways for proteins to interact?","volume":"108","author":"Keskin","year":"2008","journal-title":"Chem Rev"},{"key":"2019062808523101700_bbv009-B85","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the","volume":"25","author":"Gene","year":"2000","journal-title":"Nat Genet"},{"key":"2019062808523101700_bbv009-B86","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/nar\/27.1.254","article-title":"SCOP: a structural classification of proteins database","volume":"27","author":"Hubbard","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2019062808523101700_bbv009-B87","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2019062808523101700_bbv009-B88","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/bib\/3.3.225","article-title":"InterPro: an integrated documentation resource for protein families, domains and functional sites","volume":"3","author":"Mulder","year":"2002","journal-title":"Brief Bioinform"},{"key":"2019062808523101700_bbv009-B89","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":"2019062808523101700_bbv009-B90","first-page":"1","article-title":"Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling","volume":"6","author":"Brylinski","year":"2012","journal-title":"J Comput Sci Syst Biol"},{"key":"2019062808523101700_bbv009-B91","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","article-title":"Scoring function for automated assessment of protein structure template quality","volume":"57","author":"Zhang","year":"2004","journal-title":"Proteins"},{"key":"2019062808523101700_bbv009-B92","doi-asserted-by":"crossref","first-page":"3386","DOI":"10.1093\/bioinformatics\/btm434","article-title":"meta-PPISP: a meta web server for protein-protein interaction site prediction","volume":"23","author":"Qin","year":"2007","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B93","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1214\/aoms\/1177731944","article-title":"A comparison of alternative tests of significance for the problem of m rankings","volume":"11","author":"Friedman","year":"1940","journal-title":"Ann Math. Statist"},{"key":"2019062808523101700_bbv009-B94","doi-asserted-by":"crossref","first-page":"80","DOI":"10.2307\/3001968","article-title":"Individual comparisons by ranking methods","volume":"1","author":"Wilcoxon","year":"1945","journal-title":"Biom Bull"},{"key":"2019062808523101700_bbv009-B95","doi-asserted-by":"crossref","first-page":"3375","DOI":"10.1093\/nar\/gkm251","article-title":"LOMETS: a local meta-threading-server for protein structure prediction","volume":"35","author":"Wu","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2019062808523101700_bbv009-B96","doi-asserted-by":"crossref","first-page":"2083","DOI":"10.1093\/bioinformatics\/btr331","article-title":"Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction","volume":"27","author":"Zhang","year":"2011","journal-title":"Bioinformatics"},{"key":"2019062808523101700_bbv009-B97","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/j.str.2011.02.015","article-title":"A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds","volume":"19","author":"Chen","year":"2011","journal-title":"Structure"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/16\/6\/1025\/28880857\/bbv009.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,7]],"date-time":"2024-06-07T23:39:28Z","timestamp":1717803568000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/16\/6\/1025\/225941"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,21]]},"references-count":97,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2015,3,21]]},"published-print":{"date-parts":[[2015,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbv009","relation":{},"ISSN":["1467-5463"],"issn-type":[{"value":"1467-5463","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,11]]},"published":{"date-parts":[[2015,3,21]]}}}