{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:24:30Z","timestamp":1761863070181},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Protein-protein interactions are involved in most cellular processes, and their detailed physico-chemical and structural characterization is needed in order to understand their function at the molecular level. In-silico docking tools can complement experimental techniques, providing three-dimensional structural models of such interactions at atomic resolution. In several recent studies, protein structures have been modeled as networks (or graphs), where the nodes represent residues and the connecting edges their interactions. From such networks, it is possible to calculate different topology-based values for each of the nodes, and to identify protein regions with high centrality scores, which are known to positively correlate with key functional residues, hot spots, and protein-protein interfaces.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here we show that this correlation can be efficiently used for the scoring of rigid-body docking poses. When integrated into the pyDock energy-based docking method, the new combined scoring function significantly improved the results of the individual components as shown on a standard docking benchmark. This improvement was particularly remarkable for specific protein complexes, depending on the shape, size, type, or flexibility of the proteins involved.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The network-based representation of protein structures can be used to identify protein-protein binding regions and to efficiently score docking poses, complementing energy-based approaches.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-378","type":"journal-article","created":{"date-parts":[[2011,9,27]],"date-time":"2011-09-27T06:37:21Z","timestamp":1317105441000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Prediction of protein-binding areas by small-world residue networks and application to docking"],"prefix":"10.1186","volume":"12","author":[{"given":"Carles","family":"Pons","sequence":"first","affiliation":[]},{"given":"Fabian","family":"Glaser","sequence":"additional","affiliation":[]},{"given":"Juan","family":"Fernandez-Recio","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,9,26]]},"reference":[{"key":"4832_CR1","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1038\/nature04209","volume":"437","author":"JF Rual","year":"2005","unstructured":"Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, et al.: Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437: 1173\u20131178. 10.1038\/nature04209","journal-title":"Nature"},{"key":"4832_CR2","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1038\/nrm1859","volume":"7","author":"P Aloy","year":"2006","unstructured":"Aloy P, Russell RB: Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 2006, 7: 188\u2013197. 10.1038\/nrm1859","journal-title":"Nat Rev Mol Cell Biol"},{"key":"4832_CR3","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.sbi.2004.04.006","volume":"14","author":"RB Russell","year":"2004","unstructured":"Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A: A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004, 14: 313\u2013324. 10.1016\/j.sbi.2004.04.006","journal-title":"Curr Opin Struct Biol"},{"key":"4832_CR4","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1038\/nature06523","volume":"450","author":"CV Robinson","year":"2007","unstructured":"Robinson CV, Sali A, Baumeister W: The molecular sociology of the cell. Nature 2007, 450: 973\u2013982. 10.1038\/nature06523","journal-title":"Nature"},{"key":"4832_CR5","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1146\/annurev.biochem.77.060407.135530","volume":"77","author":"F Alber","year":"2008","unstructured":"Alber F, F\u00f6rster F, Korkin D, Topf M, Sali A: Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 2008, 77: 443\u2013477. 10.1146\/annurev.biochem.77.060407.135530","journal-title":"Annu Rev Biochem"},{"key":"4832_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2174\/138920308783565741","volume":"9","author":"DW Ritchie","year":"2008","unstructured":"Ritchie DW: Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 2008, 9: 1\u201315. 10.2174\/138920308783565741","journal-title":"Curr Protein Pept Sci"},{"key":"4832_CR7","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1006\/jmbi.1997.1203","volume":"272","author":"HA Gabb","year":"1997","unstructured":"Gabb HA, Jackson RM, Sternberg MJ: Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997, 272: 106\u2013120. 10.1006\/jmbi.1997.1203","journal-title":"J Mol Biol"},{"key":"4832_CR8","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1002\/prot.21117","volume":"65","author":"D Kozakov","year":"2006","unstructured":"Kozakov D, Brenke R, Comeau SR, Vajda S: PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 2006, 65: 392\u2013406. 10.1002\/prot.21117","journal-title":"Proteins"},{"key":"4832_CR9","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1002\/prot.21502","volume":"69","author":"J Mintseris","year":"2007","unstructured":"Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z: Integrating statistical pair potentials into protein complex prediction. Proteins 2007, 69: 511\u2013520. 10.1002\/prot.21502","journal-title":"Proteins"},{"key":"4832_CR10","doi-asserted-by":"publisher","first-page":"2544","DOI":"10.1093\/bioinformatics\/btp447","volume":"25","author":"JI Garzon","year":"2009","unstructured":"Garzon JI, Lop\u00e9z-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P: FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics 2009, 25: 2544\u20132551. 10.1093\/bioinformatics\/btp447","journal-title":"Bioinformatics"},{"key":"4832_CR11","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1002\/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4","volume":"35","author":"G Moont","year":"1999","unstructured":"Moont G, Gabb HA, Sternberg MJ: Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999, 35: 364\u2013373. 10.1002\/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4","journal-title":"Proteins"},{"key":"4832_CR12","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1002\/prot.20566","volume":"60","author":"M Zacharias","year":"2005","unstructured":"Zacharias M: ATTRACT: protein-protein docking in CAPRI using a reduced protein model. Proteins 2005, 60: 252\u2013256. 10.1002\/prot.20566","journal-title":"Proteins"},{"key":"4832_CR13","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1021\/ci100353e","volume":"51","author":"C Pons","year":"2011","unstructured":"Pons C, Talavera D, de la Cruz X, Orozco M, Fernandez-Recio J: Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. J Chem Inf Model 2011, 51: 370\u2013377. 10.1021\/ci100353e","journal-title":"J Chem Inf Model"},{"key":"4832_CR14","doi-asserted-by":"publisher","first-page":"061910","DOI":"10.1103\/PhysRevE.65.061910","volume":"65","author":"M Vendruscolo","year":"2002","unstructured":"Vendruscolo M, Dokholyan NV, Paci E, Karplus M: Small-world view of the amino acids that play a key role in protein folding. Phys Rev E Stat Nonlin Soft Matter Phys 2002, 65: 061910.","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"4832_CR15","doi-asserted-by":"publisher","first-page":"781","DOI":"10.1016\/j.jmb.2003.08.061","volume":"334","author":"LH Greene","year":"2003","unstructured":"Greene LH, Higman VA: Uncovering network systems within protein structures. J Mol Biol 2003, 334: 781\u2013791. 10.1016\/j.jmb.2003.08.061","journal-title":"J Mol Biol"},{"key":"4832_CR16","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/S0006-3495(04)74086-2","volume":"86","author":"AR Atilgan","year":"2004","unstructured":"Atilgan AR, Akan P, Baysal C: Small-world communication of residues and significance for protein dynamics. Biophys J 2004, 86: 85\u201391. 10.1016\/S0006-3495(04)74086-2","journal-title":"Biophys J"},{"key":"4832_CR17","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.physa.2004.08.046","volume":"346","author":"G Bagler","year":"2005","unstructured":"Bagler G, Sinha S: Network properties of protein structures. Physica A: Statistical Mechanics and its Applications 2005, 346: 27\u201333. 10.1016\/j.physa.2004.08.046","journal-title":"Physica A: Statistical Mechanics and its Applications"},{"key":"4832_CR18","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1038\/30918","volume":"393","author":"DJ Watts","year":"1998","unstructured":"Watts DJ, Strogatz SH: Collective dynamics of \"small-world\" networks. Nature 1998, 393: 440\u2013442. 10.1038\/30918","journal-title":"Nature"},{"key":"4832_CR19","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1002\/prot.20348","volume":"58","author":"A del Sol","year":"2005","unstructured":"del Sol A, O'Meara P: Small-world network approach to identify key residues in protein-protein interaction. Proteins 2005, 58: 672\u2013682.","journal-title":"Proteins"},{"key":"4832_CR20","doi-asserted-by":"publisher","first-page":"2120","DOI":"10.1110\/ps.062249106","volume":"15","author":"A del Sol","year":"2006","unstructured":"del Sol A, Fujihashi H, Amoros D, Nussinov R: Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci 2006, 15: 2120\u20132128. 10.1110\/ps.062249106","journal-title":"Protein Sci"},{"key":"4832_CR21","doi-asserted-by":"publisher","first-page":"e1000170","DOI":"10.1371\/journal.pcbi.1000170","volume":"4","author":"R Sathyapriya","year":"2008","unstructured":"Sathyapriya R, Vijayabaskar MS, Vishveshwara S: Insights into protein-DNA interactions through structure network analysis. PLoS Comput Biol 2008, 4: e1000170. 10.1371\/journal.pcbi.1000170","journal-title":"PLoS Comput Biol"},{"key":"4832_CR22","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1186\/1471-2105-10-341","volume":"10","author":"SR Maetschke","year":"2009","unstructured":"Maetschke SR, Yuan Z: Exploiting structural and topological information to improve prediction of RNA-protein binding sites. BMC Bioinformatics 2009, 10: 341. 10.1186\/1471-2105-10-341","journal-title":"BMC Bioinformatics"},{"key":"4832_CR23","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1016\/j.jmb.2004.10.055","volume":"344","author":"G Amitai","year":"2004","unstructured":"Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S: Network analysis of protein structures identifies functional residues. J Mol Biol 2004, 344: 1135\u20131146. 10.1016\/j.jmb.2004.10.055","journal-title":"J Mol Biol"},{"key":"4832_CR24","doi-asserted-by":"publisher","first-page":"e117","DOI":"10.1371\/journal.pcbi.0030117","volume":"3","author":"Z Hu","year":"2007","unstructured":"Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, Ma B: Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol 2007, 3: e117. 10.1371\/journal.pcbi.0030117","journal-title":"PLoS Comput Biol"},{"key":"4832_CR25","doi-asserted-by":"publisher","first-page":"e1000584","DOI":"10.1371\/journal.pcbi.1000584","volume":"5","author":"R Sathyapriya","year":"2009","unstructured":"Sathyapriya R, Duarte JM, Stehr H, Filippis I, Lappe M: Defining an essence of structure determining residue contacts in proteins. PLoS Comput Biol 2009, 5: e1000584. 10.1371\/journal.pcbi.1000584","journal-title":"PLoS Comput Biol"},{"key":"4832_CR26","doi-asserted-by":"publisher","first-page":"e1000009","DOI":"10.1371\/journal.pcbi.1000009","volume":"4","author":"HM Montiel Molina","year":"2008","unstructured":"Montiel Molina HM, Mill\u00e1n-Pacheco C, Pastor N, del Rio G: Computer-based screening of functional conformers of proteins. PLoS Comput Biol 2008, 4: e1000009. 10.1371\/journal.pcbi.1000009","journal-title":"PLoS Comput Biol"},{"key":"4832_CR27","doi-asserted-by":"publisher","first-page":"3625","DOI":"10.1007\/s00018-009-0117-0","volume":"66","author":"R Konrat","year":"2009","unstructured":"Konrat R: The protein meta-structure: a novel concept for chemical and molecular biology. Cell Mol Life Sci 2009, 66: 3625\u20133639. 10.1007\/s00018-009-0117-0","journal-title":"Cell Mol Life Sci"},{"key":"4832_CR28","doi-asserted-by":"publisher","first-page":"4641","DOI":"10.1093\/nar\/gkn433","volume":"36","author":"H David-Eden","year":"2008","unstructured":"David-Eden H, Mandel-Gutfreund Y: Revealing unique properties of the ribosome using a network based analysis. Nucleic Acids Res 2008, 36: 4641\u20134652. 10.1093\/nar\/gkn433","journal-title":"Nucleic Acids Res"},{"key":"4832_CR29","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.bpc.2007.12.005","volume":"134","author":"S Chang","year":"2008","unstructured":"Chang S, Jiao X, Li C-hua, Gong X-qi, Chen W-zu, Wang C-xin: Amino acid network and its scoring application in protein-protein docking. Biophys Chem 2008, 134: 111\u2013118. 10.1016\/j.bpc.2007.12.005","journal-title":"Biophys Chem"},{"key":"4832_CR30","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1002\/prot.21419","volume":"68","author":"TM-K Cheng","year":"2007","unstructured":"Cheng TM-K, Blundell TL, Fernandez-Recio J: pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 2007, 68: 503\u2013515. 10.1002\/prot.21419","journal-title":"Proteins"},{"key":"4832_CR31","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1002\/prot.22106","volume":"73","author":"H Hwang","year":"2008","unstructured":"Hwang H, Pierce B, Mintseris J, Janin J, Weng Z: Protein-protein docking benchmark version 3.0. Proteins 2008, 73: 705\u2013709. 10.1002\/prot.22106","journal-title":"Proteins"},{"key":"4832_CR32","doi-asserted-by":"publisher","first-page":"3111","DOI":"10.1002\/prot.22830","volume":"78","author":"H Hwang","year":"2010","unstructured":"Hwang H, Vreven T, Janin J, Weng Z: Protein-protein docking benchmark version 4.0. Proteins 2010, 78: 3111\u20133114. 10.1002\/prot.22830","journal-title":"Proteins"},{"key":"4832_CR33","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1002\/prot.22564","volume":"78","author":"C Pons","year":"2010","unstructured":"Pons C, Grosdidier S, Solernou A, P\u00e9rez-Cano L, Fern\u00e1ndez-Recio J: Present and future challenges and limitations in protein-protein docking. Proteins 2010, 78: 95\u2013108. 10.1002\/prot.22564","journal-title":"Proteins"},{"key":"4832_CR34","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1093\/protein\/gzq115","volume":"24","author":"S Mitternacht","year":"2011","unstructured":"Mitternacht S, Berezovsky IN: A geometry-based generic predictor for catalytic and allosteric sites. Protein Eng Des Sel 2011, 24: 405\u2013409. 10.1093\/protein\/gzq115","journal-title":"Protein Eng Des Sel"},{"key":"4832_CR35","doi-asserted-by":"publisher","first-page":"8637","DOI":"10.1073\/pnas.122076099","volume":"99","author":"NV Dokholyan","year":"2002","unstructured":"Dokholyan NV, Li L, Ding F, Shakhnovich EI: Topological determinants of protein folding. Proc Natl Acad Sci USA 2002, 99: 8637\u20138641. 10.1073\/pnas.122076099","journal-title":"Proc Natl Acad Sci USA"},{"key":"4832_CR36","volume-title":"Exploring network structure, dynamics, and function using networkx","author":"AANL Hagberg","year":"2008","unstructured":"Hagberg AANL, Swart PANL, S Chult DU: Exploring network structure, dynamics, and function using networkx. 2008."},{"key":"4832_CR37","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1002\/prot.21796","volume":"69","author":"S Grosdidier","year":"2007","unstructured":"Grosdidier S, Pons C, Solernou A, Fern\u00e1ndez-Recio J: Prediction and scoring of docking poses with pyDock. Proteins 2007, 69: 852\u2013858. 10.1002\/prot.21796","journal-title":"Proteins"},{"key":"4832_CR38","doi-asserted-by":"publisher","first-page":"3182","DOI":"10.1002\/prot.22773","volume":"78","author":"C Pons","year":"2010","unstructured":"Pons C, Solernou A, Perez-Cano L, Grosdidier S, Fernandez-Recio J: Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding. Proteins 2010, 78: 3182\u20133188. 10.1002\/prot.22773","journal-title":"Proteins"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-378.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T16:45:39Z","timestamp":1630514739000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-378"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,9,26]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4832"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-378","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,9,26]]},"assertion":[{"value":"30 March 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 September 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 September 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"378"}}