{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:39:29Z","timestamp":1761237569402},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2008,10,10]],"date-time":"2008-10-10T00:00:00Z","timestamp":1223596800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000191","type":"journal-article","created":{"date-parts":[[2008,10,9]],"date-time":"2008-10-09T17:09:24Z","timestamp":1223572164000},"page":"e1000191","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":39,"title":["Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes"],"prefix":"10.1371","volume":"4","author":[{"given":"Yang","family":"Shen","sequence":"first","affiliation":[]},{"given":"Ioannis Ch.","family":"Paschalidis","sequence":"additional","affiliation":[]},{"given":"Pirooz","family":"Vakili","sequence":"additional","affiliation":[]},{"given":"Sandor","family":"Vajda","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,10,10]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/35001009","article-title":"A comprehensive analysis of protein\u2013protein interactions in Saccharomyces cerevisiae.","volume":"403","author":"P Uetz","year":"2000","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1073\/pnas.061034498","article-title":"A comprehensive two-hybrid analysis to explore the yeast protein interactome.","volume":"98","author":"T Ito","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/415141a","article-title":"Functional organization of the yeast proteome by systematic analysis of protein complexes.","volume":"415","author":"AC Gavin","year":"2002","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/415180a","article-title":"Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.","volume":"415","author":"Y Ho","year":"2002","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","author":"H Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"8721","DOI":"10.1073\/pnas.89.18.8721","article-title":"Protein folding funnels: a kinetic approach to the sequence-structure relationship.","volume":"89","author":"PE Leopold","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1002\/prot.340210302","article-title":"Funnels, pathways, and the energy landscape of protein-folding: a synthesis.","volume":"21","author":"J Bryngelson","year":"1995","journal-title":"Proteins"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1110\/ps.8.6.1166","article-title":"Polymer principles and protein folding.","volume":"8","author":"KA Dill","year":"1999","journal-title":"Protein Sci"},{"key":"ref9","first-page":"1981","article-title":"Folding funnels, binding funnels, and protein function.","volume":"8","author":"CJ Tsai","year":"1999","journal-title":"Protein Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/S0959-440X(98)80046-8","article-title":"Theory of biomolecular recognition.","volume":"8","author":"JA McCammon","year":"1998","journal-title":"Curr Opin Struct Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1002\/(SICI)1097-0134(19990201)34:2<255::AID-PROT10>3.0.CO;2-O","article-title":"Protein\u2013protein recognition: exploring the energy funnels near the binding sites.","volume":"34","author":"C Zhang","year":"1999","journal-title":"Proteins"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1110\/ps.8701","article-title":"How common is the funnel-like energy landscape in protein\u2013protein interactions?","volume":"10","author":"A Tovchigrechko","year":"2001","journal-title":"Protein Sci"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1002\/prot.1139","article-title":"New insights into the mechanism of protein\u2013protein association.","volume":"45","author":"T Selzer","year":"2001","journal-title":"Proteins"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"8011","DOI":"10.1073\/pnas.95.14.8011","article-title":"Reaching the global minimum in docking simulations: a monte carlo energy minimization approach using bezier splines.","volume":"95","author":"JY Trosset","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1016\/S0006-3495(99)77281-4","article-title":"Free energy landscapes of encounter complexes in protein\u2013protein association.","volume":"76","author":"CJ Camacho","year":"1999","journal-title":"Biophys J"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1016\/S0006-3495(00)76668-9","article-title":"Kinetics of desolvation-mediated protein\u2013protein binding.","volume":"78","author":"CJ Camacho","year":"2000","journal-title":"Biophys J"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1002\/prot.10393","article-title":"Assessment of blind predictions of protein\u2013protein interactions: current status of docking methods.","volume":"52","author":"R M\u00e9ndez","year":"2003","journal-title":"Proteins"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1002\/prot.20551","article-title":"Assessment of CAPRI predictions in rounds 3\u20135 shows progress in docking procedures.","volume":"60","author":"R M\u00e9ndez","year":"2005","journal-title":"Proteins"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1002\/prot.21804","article-title":"Docking and scoring protein complexes: CAPRI 3rd edition.","volume":"69","author":"MF Lensink","year":"2007","journal-title":"Proteins"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.tibtech.2004.01.006","article-title":"Protein\u2013protein docking: is the glass half full or half empty?","volume":"22","author":"S Vajda","year":"2004","journal-title":"Trends Biotechnol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1002\/prot.10389","article-title":"ZDOCK: an initial-stage protein docking algorithm.","volume":"52","author":"R Chen","year":"2003","journal-title":"Proteins"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1002\/prot.21117","article-title":"PIPER: an FFT-based protein docking program with pairwise potentials.","volume":"65","author":"D Kozakov","year":"2006","journal-title":"Proteins"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/S0022-2836(95)80063-8","article-title":"A geometry-based suite of molecular docking processes.","volume":"248","author":"D Fischer","year":"1995","journal-title":"J Mol Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0022-2836(03)00670-3","article-title":"Protein\u2013protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.","volume":"331","author":"JJ Gray","year":"2003","journal-title":"J Mol Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1006\/jmbi.1994.1052","article-title":"Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.","volume":"235","author":"R Abagyan","year":"1994","journal-title":"J Mol Biol"},{"key":"ref26","first-page":"1","article-title":"Convex global underestimation for molecular structure prediction.","author":"AT Phillips","year":"2001"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1089\/cmb.1997.4.227","article-title":"Protein structure and energy landscape dependence on sequence using a continuous energy function.","volume":"4","author":"KA Dill","year":"1997","journal-title":"J Comput Biol"},{"key":"ref28","first-page":"280","article-title":"Coupled optimization in protein docking.","author":"JC Mitchell","year":"1999"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1002\/jcc.10026","article-title":"Semi-global simplex optimization and its application to deter-mining the preferred solvation sites of proteins.","volume":"23","author":"S Dennis","year":"2002","journal-title":"J Comput Chem"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1109\/TAC.2007.894518","article-title":"A semi-definite programming-based underestimation method for stochastic global optimization in protein docking.","volume":"52","author":"IC Paschalidis","year":"2007","journal-title":"IEEE Trans Automat Contr"},{"key":"ref31","first-page":"3675","article-title":"A semi-definite programming-based underestimation method for global optimization in molecular docking.","author":"IC Paschalidis","year":"2005"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/bioinformatics\/btg371","article-title":"ClusPro: an automated docking and discrimination method for the prediction of protein complexes.","volume":"20","author":"SR Comeau","year":"2004","journal-title":"Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1109\/TRA.2002.807530","article-title":"Numerical optimization on the Euclidean group with applications to camera calibration.","volume":"19","author":"S Gwak","year":"2003","journal-title":"IEEE Trans Robot Autom"},{"key":"ref34","first-page":"5330","article-title":"Protein\u2013protein docking with reduced potentials by exploiting multi-dimensional energy funnels.","author":"IC Paschalidis","year":"2006"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1145\/256157.256160","article-title":"Smooth invariant interpolation of rotations.","volume":"16","author":"FC Park","year":"1997","journal-title":"ACM Trans Graph"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1115\/1.2826116","article-title":"Distance metrics on the rigid-body motions with applications to mechanism design.","volume":"117","author":"FC Park","year":"1995","journal-title":"J Mech Des"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1146\/annurev.bb.14.060185.001023","article-title":"Diffusion-controlled macromolecular interactions.","volume":"14","author":"OG Berg","year":"1985","journal-title":"Annu Rev Biophys Biophys Chem"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1002\/prot.10390","article-title":"A protein\u2013protein docking benchmark.","volume":"52","author":"R Chen","year":"2003","journal-title":"Proteins"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1002\/prot.20560","article-title":"Protein\u2013protein docking benchmark 2.0: an update.","volume":"60","author":"J Mintseris","year":"2005","journal-title":"Proteins"},{"key":"ref40","first-page":"629","article-title":"RDOCK: refinement of rigid-body protein docking predictions.","volume":"53","author":"L Li","year":"2003","journal-title":"Proteins"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"W233","DOI":"10.1093\/nar\/gkn216","article-title":"The RosettaDock server for local protein\u2013protein docking.","volume":"36","author":"S Lyskov","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0022-2836(03)00670-3","article-title":"Protein\u2013protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.","volume":"331","author":"JJ Gray","year":"2003","journal-title":"J Mol Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1002\/prot.21754","article-title":"Docking with PIPER and refinement with SDU in rounds 6\u201311 of CAPRI.","volume":"69","author":"Y Shen","year":"2007","journal-title":"Proteins"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1080\/00207170701203756","article-title":"Global optimization in protein docking us-ing convex underestimation and semidefinite programming.","volume":"22","author":"RF Marcia","year":"2007","journal-title":"Optim Methods Softw"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1529\/biophysj.104.058768","article-title":"Optimal clustering for detecting near-native conformation in protein docking.","volume":"89","author":"D Kozakov","year":"2005","journal-title":"Biophys J"},{"key":"ref46","article-title":"Convex Optimization","author":"S Boyd","year":"2003"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1080\/10556789908805766","article-title":"Using SeDuMi 1.02, a MATLAB toolbox for optimization over symmet-ric cones.","volume":"11\u201312","author":"JF Sturm","year":"1999","journal-title":"Optim Methods Softw"},{"key":"ref48","article-title":"SDPA (SemiDefinite Programming Algorithm) User&apos;s Manual Version 6.00. Department of Mathematical and Com-puting Sciences, Tokyo Institute of Technology.","author":"K Fujisawa","year":"2002"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1006\/jmbi.1996.0859","article-title":"Determination of atomic desolvation energies from the structures of crystallized proteins.","volume":"267","author":"C Zhang","year":"1997","journal-title":"J Mol Biol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1021\/ma00145a039","article-title":"Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation.","volume":"18","author":"S Miyazawa","year":"1985","journal-title":"Macromolecules"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/jcc.540040211","article-title":"CHARMM: a program for macromolecular energy, minimization, and dynamics calculations.","volume":"4","author":"BR Brooks","year":"1983","journal-title":"J Comput Chem"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000191","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T10:30:54Z","timestamp":1557829854000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000191"}},"subtitle":[],"editor":[{"given":"Matthew P.","family":"Jacobson","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,10,10]]},"references-count":51,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2008,10,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000191","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,10]]}}}