{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T23:08:00Z","timestamp":1781737680933,"version":"3.54.5"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The atomic structures of protein\u2013protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.<\/jats:p>\n               <jats:p>Availability and implementation: The server does not require registration by the user and is freely available for non-commercial academic use at http:\/\/life.bsc.es\/pid\/ccharppi<\/jats:p>\n               <jats:p>Contact: \u00a0juanf@bsc.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu594","type":"journal-article","created":{"date-parts":[[2014,9,3]],"date-time":"2014-09-03T06:17:49Z","timestamp":1409725069000},"page":"123-125","source":"Crossref","is-referenced-by-count":75,"title":["CCharPPI web server: computational characterization of protein\u2013protein interactions from structure"],"prefix":"10.1093","volume":"31","author":[{"given":"Iain H.","family":"Moal","sequence":"first","affiliation":[{"name":"Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, C\/Jordi Girona 29, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Jim\u00e9nez-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, C\/Jordi Girona 29, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Fern\u00e1ndez-Recio","sequence":"additional","affiliation":[{"name":"Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, C\/Jordi Girona 29, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,9,2]]},"reference":[{"key":"2023020116151072300_btu594-B1","doi-asserted-by":"crossref","first-page":"e1003216","DOI":"10.1371\/journal.pcbi.1003216","article-title":"Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization","volume":"9","author":"Agius","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"2023020116151072300_btu594-B2","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/prot.21495","article-title":"FireDock: fast interaction refinement in molecular docking","volume":"69","author":"Andrusier","year":"2007","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B3","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1093\/bioinformatics\/btq007","article-title":"PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta","volume":"26","author":"Chaudhury","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020116151072300_btu594-B4","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1002\/prot.21419","article-title":"pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking","volume":"68","author":"Cheng","year":"2007","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B5","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/256705a0","article-title":"Principles of protein-protein recognition","volume":"256","author":"Chothia","year":"1975","journal-title":"Nature"},{"key":"2023020116151072300_btu594-B6","doi-asserted-by":"crossref","first-page":"4217","DOI":"10.1529\/biophysj.108.135814","article-title":"DARS (Decoys As the Reference State) potentials for protein-protein docking","volume":"95","author":"Chuang","year":"2008","journal-title":"Biophys. J."},{"key":"2023020116151072300_btu594-B7","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1002\/pro.585","article-title":"On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking","volume":"20","author":"Feliu","year":"2011","journal-title":"Protein Sci."},{"key":"2023020116151072300_btu594-B8","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1186\/1471-2105-11-92","article-title":"Potentials\u2019R\u2019 Us web-server for protein energy estimations with coarse-grained knowledge-based potentials","volume":"11","author":"Feng","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020116151072300_btu594-B9","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.jmb.2011.09.031","article-title":"Community-wide assessment of protein-interface modeling suggests improvements to design methodology","volume":"414","author":"Fleishman","year":"2011","journal-title":"J. Mol. Biol."},{"key":"2023020116151072300_btu594-B10","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":"2023020116151072300_btu594-B11","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":"2023020116151072300_btu594-B12","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1002\/pro.580","article-title":"A structure-based benchmark for protein-protein binding affinity","volume":"20","author":"Kastritis","year":"2011","journal-title":"Protein Sci."},{"key":"2023020116151072300_btu594-B13","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":"2023020116151072300_btu594-B14","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1186\/1471-2105-12-280","article-title":"DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking","volume":"12","author":"Liu","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020116151072300_btu594-B15","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1002\/prot.20019","article-title":"A physical reference state unifies the structure-derived potential of mean force for protein folding and binding","volume":"56","author":"Liu","year":"2004","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B16","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1016\/S0006-3495(03)74997-2","article-title":"Development of unified statistical potentials describing protein-protein interactions","volume":"84","author":"Lu","year":"2003","journal-title":"Biophys. J."},{"key":"2023020116151072300_btu594-B17","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.jmb.2007.11.033","article-title":"OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing","volume":"376","author":"Lu","year":"2008","journal-title":"J. Mol. Biol."},{"key":"2023020116151072300_btu594-B18","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1002\/prot.21502","article-title":"Integrating statistical pair potentials into protein complex prediction","volume":"69","author":"Mintseris","year":"2007","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B19","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1016\/j.febslet.2010.02.021","article-title":"New measures for estimating surface complementarity and packing at protein-protein interfaces","volume":"584","author":"Mitra","year":"2010","journal-title":"FEBS Lett."},{"key":"2023020116151072300_btu594-B20","doi-asserted-by":"crossref","first-page":"e1002351","DOI":"10.1371\/journal.pcbi.1002351","article-title":"Kinetic rate constant prediction supports the conformational selection mechanism of protein binding","volume":"8","author":"Moal","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"2023020116151072300_btu594-B21","doi-asserted-by":"crossref","first-page":"2600","DOI":"10.1093\/bioinformatics\/bts489","article-title":"SKEMPI: a Structural kinetic and energetic database of mutant protein interactions and its use in empirical models","volume":"28","author":"Moal","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020116151072300_btu594-B22","doi-asserted-by":"crossref","first-page":"3715","DOI":"10.1021\/ct400295z","article-title":"Intermolecular contact potentials for protein-protein interactions extracted from binding free energy changes upon mutation","volume":"9","author":"Moal","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"2023020116151072300_btu594-B23","doi-asserted-by":"crossref","first-page":"3002","DOI":"10.1093\/bioinformatics\/btr513","article-title":"Protein-protein binding affinity prediction on a diverse set of structures","volume":"27","author":"Moal","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020116151072300_btu594-B24","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1016\/j.sbi.2013.06.017","article-title":"Scoring functions for protein-protein interactions","volume":"23","author":"Moal","year":"2013","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023020116151072300_btu594-B25","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1186\/1471-2105-14-286","article-title":"The scoring of poses in protein-protein docking: current capabilities and future directions","volume":"14","author":"Moal","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023020116151072300_btu594-B26","doi-asserted-by":"crossref","first-page":"1980","DOI":"10.1002\/prot.24356","article-title":"Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions","volume":"81","author":"Moretti","year":"2013","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B27","doi-asserted-by":"crossref","first-page":"2192","DOI":"10.1002\/prot.24387","article-title":"Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges","volume":"81","author":"Pallara","year":"2013","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B28","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1002\/prot.21373","article-title":"ZRANK: reranking protein docking predictions with an optimized energy function","volume":"67","author":"Pierce","year":"2007","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B29","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1002\/prot.21920","article-title":"A combination of rescoring and refinement significantly improves protein docking performance","volume":"72","author":"Pierce","year":"2008","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B30","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1002\/prot.20380","article-title":"Inferring ideal amino acid interaction forms from statistical protein contact potentials","volume":"59","author":"Pokarowski","year":"2005","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B31","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1021\/ci100353e","article-title":"Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking","volume":"51","author":"Pons","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"2023020116151072300_btu594-B32","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1002\/prot.21149","article-title":"A novel high resolution Calpha\u2013Calpha distance dependent force field based on a high quality decoy set","volume":"65","author":"Rajgaria","year":"2006","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B33","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1002\/prot.21561","article-title":"Distance dependent centroid to centroid force fields using high resolution decoys","volume":"70","author":"Rajgaria","year":"2008","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B34","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1002\/prot.22550","article-title":"PIE-efficient filters and coarse grained potentials for unbound protein-protein docking","volume":"78","author":"Ravikant","year":"2010","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B35","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1110\/ps.062416606","article-title":"Statistical potential for assessment and prediction of protein structures","volume":"15","author":"Shen","year":"2006","journal-title":"Protein Sci."},{"key":"2023020116151072300_btu594-B36","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1472-6807-10-40","article-title":"Designing coarse grained-and atom based-potentials for protein-protein docking","volume":"10","author":"Tobi","year":"2010","journal-title":"BMC Struct. Biol."},{"key":"2023020116151072300_btu594-B37","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1002\/prot.20859","article-title":"Optimal design of protein docking potentials: efficiency and limitations","volume":"62","author":"Tobi","year":"2006","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B38","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/bib\/bbp001","article-title":"A survey of available tools and web servers for analysis of protein-protein interactions and interfaces","volume":"10","author":"Tuncbag","year":"2009","journal-title":"Brief. Bioinformatics"},{"key":"2023020116151072300_btu594-B39","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1002\/prot.24214","article-title":"Improving ranking of models for protein complexes with side chain modeling and atomic potentials","volume":"81","author":"Viswanath","year":"2013","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B40","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1110\/ps.033480.107","article-title":"Ab initio\n               folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions","volume":"17","author":"Yang","year":"2008","journal-title":"Protein Sci."},{"key":"2023020116151072300_btu594-B41","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1002\/prot.21968","article-title":"Specific interactions for ab initio folding of protein terminal regions with secondary structures","volume":"72","author":"Yang","year":"2008","journal-title":"Proteins"},{"key":"2023020116151072300_btu594-B42","doi-asserted-by":"crossref","first-page":"e33340","DOI":"10.1371\/journal.pone.0033340","article-title":"Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface","volume":"7","author":"Yu","year":"2012","journal-title":"PLoS One"},{"key":"2023020116151072300_btu594-B43","doi-asserted-by":"crossref","first-page":"e15386","DOI":"10.1371\/journal.pone.0015386","article-title":"A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction","volume":"5","author":"Zhang","year":"2010","journal-title":"PLoS One"},{"key":"2023020116151072300_btu594-B44","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1016\/j.bpj.2011.09.012","article-title":"GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction","volume":"101","author":"Zhou","year":"2011","journal-title":"Biophys. J."},{"key":"2023020116151072300_btu594-B45","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"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/1\/123\/49010922\/bioinformatics_31_1_123.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/1\/123\/49010922\/bioinformatics_31_1_123.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:24:29Z","timestamp":1675297469000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/1\/123\/2365710"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9,2]]},"references-count":45,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu594","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,1]]},"published":{"date-parts":[[2014,9,2]]}}}