{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:30:54Z","timestamp":1787009454032,"version":"3.56.0"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1223,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"DOI":"10.1093\/nar\/gkt450","type":"journal-article","created":{"date-parts":[[2013,5,31]],"date-time":"2013-05-31T00:24:30Z","timestamp":1369959870000},"page":"W333-W339","source":"Crossref","is-referenced-by-count":356,"title":["BeAtMuSiC: prediction of changes in protein\u2013protein binding affinity on mutations"],"prefix":"10.1093","volume":"41","author":[{"given":"Yves","family":"Dehouck","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean Marc","family":"Kwasigroch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marianne","family":"Rooman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimitri","family":"Gilis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,5,30]]},"reference":[{"key":"key\n\t\t\t\t20171013122937_gkt450-B1","doi-asserted-by":"crossref","first-page":"4630","DOI":"10.2174\/138161212802651553","article-title":"Modulating protein-protein interactions: from structural determinants of binding to druggability prediction to application","volume":"18","author":"Metz","year":"2012","journal-title":"Curr. Pharm. Des."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B2","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.sbi.2009.07.005","article-title":"Computational design of affinity and specificity at protein-protein interfaces","volume":"19","author":"Karanicolas","year":"2009","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B3","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1073\/pnas.93.1.13","article-title":"Principles of protein-protein interactions","volume":"93","author":"Jones","year":"1996","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B4","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1002\/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H","article-title":"Residue frequencies and pairing preferences at protein-protein interfaces","volume":"43","author":"Glaser","year":"2001","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B5","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1002\/prot.10085","article-title":"Dissecting protein-protein recognition sites","volume":"47","author":"Chakrabarti","year":"2002","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B6","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/S0022-2836(02)01223-8","article-title":"Analysing six types of protein-protein interfaces","volume":"325","author":"Ofran","year":"2003","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B7","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.sbi.2007.01.004","article-title":"The molecular architecture of protein-protein binding sites","volume":"17","author":"Reichmann","year":"2007","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B8","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1007\/s00018-007-7451-x","article-title":"The interface of protein-protein complexes: analysis of contacts and prediction of interactions","volume":"65","author":"Bahadur","year":"2008","journal-title":"Cell. Mol. Life Sci."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B9","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1039\/b904161n","article-title":"Energy based approach for understanding the recognition mechanism in protein-protein complexes","volume":"5","author":"Gromiha","year":"2009","journal-title":"Mol. Biosyst."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B10","doi-asserted-by":"crossref","first-page":"035002","DOI":"10.1088\/1478-3975\/8\/3\/035002","article-title":"The diversity of physical forces and mechanisms in intermolecular interactions","volume":"8","author":"Berezovsky","year":"2011","journal-title":"Phys. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B11","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1002\/prot.21396","article-title":"Hot spots\u2013a review of the protein-protein interface determinant amino-acid residues","volume":"68","author":"Moreira","year":"2007","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B12","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":"key\n\t\t\t\t20171013122937_gkt450-B13","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.2174\/138161212799436412","article-title":"Computational prediction of protein hot spot residues","volume":"18","author":"Morrow","year":"2012","journal-title":"Curr. Pharm. Des."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B14","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/0076-6879(91)02020-A","article-title":"Systematic mutational analyses of protein-protein interfaces","volume":"202","author":"Wells","year":"1991","journal-title":"Methods Enzymol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B15","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1093\/bioinformatics\/17.3.284","article-title":"ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions","volume":"17","author":"Thorn","year":"2001","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B16","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1002\/prot.20348","article-title":"Small-world network approach to identify key residues in protein-protein interaction","volume":"58","author":"del Sol","year":"2005","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B17","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1741-7007-5-43","article-title":"Spatial chemical conservation of hot spot interactions in protein-protein complexes","volume":"5","author":"Shulman-Peleg","year":"2007","journal-title":"BMC Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B18","doi-asserted-by":"crossref","first-page":"e119","DOI":"10.1371\/journal.pcbi.0030119","article-title":"Protein-protein interaction hotspots carved into sequences","volume":"3","author":"Ofran","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B19","doi-asserted-by":"crossref","first-page":"W265","DOI":"10.1093\/nar\/gkn346","article-title":"KFC Server: interactive forecasting of protein interaction hot spots","volume":"36","author":"Darnell","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B20","doi-asserted-by":"crossref","first-page":"D662","DOI":"10.1093\/nar\/gkm813","article-title":"HotSprint: database of computational hot spots in protein interfaces","volume":"36","author":"Guney","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B21","doi-asserted-by":"crossref","first-page":"i207","DOI":"10.1093\/bioinformatics\/btn268","article-title":"Comprehensive in silico mutagenesis highlights functionally important residues in proteins","volume":"24","author":"Bromberg","year":"2008","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B22","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1186\/1471-2105-9-447","article-title":"Identification of hot-spot residues in protein-protein interactions by computational docking","volume":"9","author":"Grosdidier","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B23","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1186\/1471-2105-10-365","article-title":"Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods","volume":"10","author":"Lise","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B24","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1093\/nar\/gkp132","article-title":"A feature-based approach to modeling protein-protein interaction hot spots","volume":"37","author":"Cho","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B25","doi-asserted-by":"crossref","first-page":"W402","DOI":"10.1093\/nar\/gkq323","article-title":"HotPoint: hot spot prediction server for protein interfaces","volume":"38","author":"Tuncbag","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B26","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1186\/1471-2105-11-174","article-title":"APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility","volume":"11","author":"Xia","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B27","doi-asserted-by":"crossref","first-page":"e86","DOI":"10.1093\/nar\/gkp1158","article-title":"PCRPi: presaging critical residues in protein interfaces, a new computational tool to chart hot spots in protein interfaces","volume":"38","author":"Assi","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B28","doi-asserted-by":"crossref","first-page":"2671","DOI":"10.1002\/prot.23094","article-title":"KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features","volume":"79","author":"Zhu","year":"2011","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B29","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/protein\/gzr066","article-title":"Prediction of hot spots in protein interfaces using a random forest model with hybrid features","volume":"25","author":"Wang","year":"2012","journal-title":"Protein Eng. Des. Sel."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B30","doi-asserted-by":"crossref","first-page":"8133","DOI":"10.1021\/ja990935j","article-title":"Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies","volume":"121","author":"Massova","year":"1999","journal-title":"J. Am. Chem. Soc."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B31","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1002\/jcc.1153","article-title":"Computational alanine scanning of the 1:1 human growth hormone-receptor complex","volume":"23","author":"Huo","year":"2002","journal-title":"J. Comput. Chem."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B32","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1002\/jcc.20566","article-title":"Computational alanine scanning mutagenesis\u2013an improved methodological approach","volume":"28","author":"Moreira","year":"2007","journal-title":"J. Comput. Chem."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B33","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1093\/protein\/gzq047","article-title":"Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction","volume":"24","author":"Bradshaw","year":"2011","journal-title":"Protein Eng. Des. Sel."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B34","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S0022-2836(02)00442-4","article-title":"Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations","volume":"320","author":"Guerois","year":"2002","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B35","doi-asserted-by":"crossref","first-page":"14116","DOI":"10.1073\/pnas.202485799","article-title":"A simple physical model for binding energy hot spots in protein-protein interactions","volume":"99","author":"Kortemme","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B36","doi-asserted-by":"crossref","first-page":"pl2","DOI":"10.1126\/stke.2192004pl2","article-title":"Computational alanine scanning of protein-protein interfaces","volume":"2004","author":"Kortemme","year":"2004","journal-title":"Sci. STKE"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B37","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.jmb.2004.12.019","article-title":"Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity","volume":"347","author":"Pokala","year":"2005","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B38","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1063\/1.4730653","article-title":"Design of modified proteins using knowledge-based approaches","volume":"1456","author":"Dehouck","year":"2012","journal-title":"AIP Conf. Proc."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B39","doi-asserted-by":"crossref","first-page":"2600","DOI":"10.1093\/bioinformatics\/bts489","article-title":"SKEMPI: a structural and energetic database of mutant protein interactions and its use in empirical models","volume":"28","author":"Moal","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B40","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":"key\n\t\t\t\t20171013122937_gkt450-B41","doi-asserted-by":"crossref","first-page":"4010","DOI":"10.1529\/biophysj.105.079434","article-title":"A new generation of statistical potentials for proteins","volume":"90","author":"Dehouck","year":"2006","journal-title":"Biophys. J."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B42","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/btp445","article-title":"Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0","volume":"25","author":"Dehouck","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B43","doi-asserted-by":"crossref","first-page":"035003","DOI":"10.1088\/1478-3975\/8\/3\/035003","article-title":"The expanding view of protein-protein interactions: complexes involving intrinsically disordered proteins","volume":"8","author":"M\u00e9sz\u00e1ros","year":"2011","journal-title":"Phys. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B44","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1006\/jmbi.1999.2757","article-title":"Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases","volume":"289","author":"Krowarsch","year":"1999","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B45","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1126\/science.1202617","article-title":"Computational design of proteins targeting the conserved stem region of influenza hemagglutinin","volume":"332","author":"Fleishman","year":"2011","journal-title":"Science"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B46","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/nbt.2214","article-title":"Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing","volume":"30","author":"Whitehead","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t20171013122937_gkt450-B47","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":"key\n\t\t\t\t20171013122937_gkt450-B48","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":"key\n\t\t\t\t20171013122937_gkt450-B49","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1126\/science.4023714","article-title":"Hydrophobicity of amino acid residues in globular proteins","volume":"229","author":"Rose","year":"1985","journal-title":"Science"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B50","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/1471-2105-12-151","article-title":"PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality","volume":"12","author":"Dehouck","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013122937_gkt450-B51","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.jbiotec.2012.06.020","article-title":"Structure-based mutant stability predictions on proteins of unknown structure","volume":"161","author":"Gonnelli","year":"2012","journal-title":"J. Biotechnol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/W1\/W333\/3861245\/gkt450.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T04:07:50Z","timestamp":1645589270000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/W1\/W333\/1106169\/BeAtMuSiC-prediction-of-changes-in-proteinprotein"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,30]]},"references-count":51,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2013,5,30]]},"published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkt450","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,1]]},"published":{"date-parts":[[2013,5,30]]}}}