{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T09:54:00Z","timestamp":1790157240103,"version":"4.0.1"},"reference-count":93,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2015,7,24]],"date-time":"2015-07-24T00:00:00Z","timestamp":1437696000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001870","name":"Foundation For Polish Science","doi-asserted-by":"publisher","award":["TEAM\/2011-7\/6"],"award-info":[{"award-number":["TEAM\/2011-7\/6"]}],"id":[{"id":"10.13039\/501100001870","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Center","award":["2014\/14\/A\/ST6\/00088"],"award-info":[{"award-number":["2014\/14\/A\/ST6\/00088"]}]},{"name":"Polish Ministry of Science and Higher Education","award":["IP2012 016872"],"award-info":[{"award-number":["IP2012 016872"]}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Methods"],"published-print":{"date-parts":[[2016,1]]},"DOI":"10.1016\/j.ymeth.2015.07.004","type":"journal-article","created":{"date-parts":[[2015,7,10]],"date-time":"2015-07-10T13:42:44Z","timestamp":1436535764000},"page":"72-83","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":152,"special_numbering":"C","title":["Modeling of protein\u2013peptide interactions using the CABS-dock web server for binding site search and flexible docking"],"prefix":"10.1016","volume":"93","author":[{"given":"Maciej","family":"Blaszczyk","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mateusz","family":"Kurcinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maksim","family":"Kouza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukasz","family":"Wieteska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksander","family":"Debinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrzej","family":"Kolinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Kmiecik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ymeth.2015.07.004_b0005","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.copbio.2008.06.004","article-title":"Peptide-mediated interactions in biological systems: new discoveries and applications","volume":"19","author":"Petsalaki","year":"2008","journal-title":"Curr. Opin. Biotechnol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0010","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1016\/j.sbi.2013.07.006","article-title":"Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how","volume":"23","author":"London","year":"2013","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0015","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1007\/978-1-61779-588-6_17","article-title":"Modeling peptide\u2013protein interactions","volume":"857","author":"London","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0020","doi-asserted-by":"crossref","first-page":"34250","DOI":"10.1074\/jbc.M114.571182","article-title":"Interferon regulatory factor 8 (IRF8) interacts with the B cell lymphoma 6 (BCL6) corepressor BCOR","volume":"289","author":"Yoon","year":"2014","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.ymeth.2015.07.004_b0025","first-page":"1145","article-title":"Homer proteins mediate the interaction between STIM1 and Ca1.2 channels","volume":"2015","author":"Dionisio","year":"1853","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.ymeth.2015.07.004_b0030","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1073\/pnas.0507493103","article-title":"Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy","volume":"103","author":"Tovar","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ymeth.2015.07.004_b0035","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.4049\/jimmunol.179.3.1559","article-title":"Spontaneous and prostatic steroid binding protein peptide-induced autoimmune prostatitis in the nonobese diabetic mouse","volume":"179","author":"Penna","year":"2007","journal-title":"J. Immunol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0040","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.4155\/fmc.12.99","article-title":"Recent work in the development and application of protein-peptide docking","volume":"4","author":"Audie","year":"2012","journal-title":"Future Med. Chem."},{"key":"10.1016\/j.ymeth.2015.07.004_b0045","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1110\/ps.04964705","article-title":"A computational method for the analysis and prediction of protein:phosphopeptide-binding sites","volume":"14","author":"Joughin","year":"2005","journal-title":"Protein Sci."},{"key":"10.1016\/j.ymeth.2015.07.004_b0050","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.1371\/journal.pcbi.0030182","article-title":"Structure-templated predictions of novel protein interactions from sequence information","volume":"3","author":"Betel","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0055","doi-asserted-by":"crossref","first-page":"e796","DOI":"10.1371\/journal.pone.0000796","article-title":"NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence","volume":"2","author":"Nielsen","year":"2007","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ymeth.2015.07.004_b0060","doi-asserted-by":"crossref","first-page":"e1000052","DOI":"10.1371\/journal.pcbi.1000052","article-title":"Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm","volume":"4","author":"Sanchez","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0065","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.str.2013.02.023","article-title":"Protein\u2013peptide complex prediction through fragment interaction patterns","volume":"21","author":"Verschueren","year":"2013","journal-title":"Structure"},{"key":"10.1016\/j.ymeth.2015.07.004_b0070","doi-asserted-by":"crossref","first-page":"W423","DOI":"10.1093\/nar\/gks398","article-title":"PepSite: prediction of peptide-binding sites from protein surfaces","volume":"40","author":"Trabuco","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2015.07.004_b0075","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1002\/prot.24422","article-title":"Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions","volume":"81","author":"Lavi","year":"2013","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0080","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1002\/prot.22629","article-title":"DynaDock: a new molecular dynamics-based algorithm for protein\u2013peptide docking including receptor flexibility","volume":"78","author":"Antes","year":"2010","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0085","doi-asserted-by":"crossref","first-page":"W249","DOI":"10.1093\/nar\/gkr431","article-title":"Rosetta FlexPepDock web server-high resolution modeling of peptide\u2013protein interactions","volume":"39","author":"London","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2015.07.004_b0090","doi-asserted-by":"crossref","first-page":"e18934","DOI":"10.1371\/journal.pone.0018934","article-title":"Rosetta FlexPepDock ab initio: simultaneous folding, docking and refinement of peptides onto their receptors","volume":"6","author":"Raveh","year":"2011","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ymeth.2015.07.004_b0095","doi-asserted-by":"crossref","first-page":"e58769","DOI":"10.1371\/journal.pone.0058769","article-title":"A unified conformational selection and induced fit approach to protein\u2013peptide docking","volume":"8","author":"Trellet","year":"2013","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ymeth.2015.07.004_b0100","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/978-1-4939-2285-7_10","article-title":"Information-driven modeling of protein\u2013peptide complexes","volume":"1268","author":"Trellet","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0105","doi-asserted-by":"crossref","first-page":"2836","DOI":"10.1093\/bioinformatics\/btr498","article-title":"PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors","volume":"27","author":"Donsky","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ymeth.2015.07.004_b0110","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1016\/j.str.2011.09.014","article-title":"Structural and dynamic determinants of protein\u2013peptide recognition","volume":"19","author":"Dagliyan","year":"2011","journal-title":"Structure"},{"key":"10.1016\/j.ymeth.2015.07.004_b0115","doi-asserted-by":"crossref","first-page":"e1000335","DOI":"10.1371\/journal.pcbi.1000335","article-title":"Accurate prediction of peptide binding sites on protein surfaces","volume":"5","author":"Petsalaki","year":"2009","journal-title":"PLoS Comput. Biol."},{"issue":"W1","key":"10.1016\/j.ymeth.2015.07.004_b0120","doi-asserted-by":"crossref","first-page":"W419","DOI":"10.1093\/nar\/gkv456","article-title":"CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site","volume":"43","author":"Kurcinski","year":"2015","journal-title":"Nucleic Acids Res."},{"issue":"33\u201338","key":"10.1016\/j.ymeth.2015.07.004_b0125","first-page":"27","article-title":"VMD: visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"10.1016\/j.ymeth.2015.07.004_b0130","doi-asserted-by":"crossref","first-page":"349","DOI":"10.18388\/abp.2004_3575","article-title":"Protein modeling and structure prediction with a reduced representation","volume":"51","author":"Kolinski","year":"2004","journal-title":"Acta Biochim. Pol."},{"issue":"Suppl 7","key":"10.1016\/j.ymeth.2015.07.004_b0135","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1002\/prot.20723","article-title":"Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models","volume":"61","author":"Kolinski","year":"2005","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0140","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1002\/prot.21049","article-title":"STRUCTFAST: protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring","volume":"64","author":"Debe","year":"2006","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0145","doi-asserted-by":"crossref","first-page":"W406","DOI":"10.1093\/nar\/gkt462","article-title":"CABS-fold: server for the de novo and consensus-based prediction of protein structure","volume":"41","author":"Blaszczyk","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2015.07.004_b0150","doi-asserted-by":"crossref","first-page":"131","DOI":"10.18388\/abp.2006_3371","article-title":"Denatured proteins and early folding intermediates simulated in a reduced conformational space","volume":"53","author":"Kmiecik","year":"2006","journal-title":"Acta Biochim. Pol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0155","doi-asserted-by":"crossref","first-page":"12330","DOI":"10.1073\/pnas.0702265104","article-title":"Characterization of protein-folding pathways by reduced-space modeling","volume":"104","author":"Kmiecik","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ymeth.2015.07.004_b0160","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1529\/biophysj.107.116095","article-title":"Folding pathway of the b1 domain of protein G explored by multiscale modeling","volume":"94","author":"Kmiecik","year":"2008","journal-title":"Biophys. J."},{"key":"10.1016\/j.ymeth.2015.07.004_b0165","series-title":"Multiscale Approaches to Protein Modeling","first-page":"281","author":"Kmiecik","year":"2011"},{"key":"10.1016\/j.ymeth.2015.07.004_b0170","doi-asserted-by":"crossref","first-page":"7026","DOI":"10.1021\/jp301720w","article-title":"From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A","volume":"116","author":"Kmiecik","year":"2012","journal-title":"J. Phys. Chem. B"},{"key":"10.1016\/j.ymeth.2015.07.004_b0175","doi-asserted-by":"crossref","first-page":"10283","DOI":"10.1021\/ja203275f","article-title":"Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism","volume":"133","author":"Kmiecik","year":"2011","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.ymeth.2015.07.004_b0180","doi-asserted-by":"crossref","first-page":"9893","DOI":"10.3390\/ijms14059893","article-title":"Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics","volume":"14","author":"Wabik","year":"2013","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.ymeth.2015.07.004_b0185","doi-asserted-by":"crossref","first-page":"W427","DOI":"10.1093\/nar\/gkt332","article-title":"CABS-flex: server for fast simulation of protein structure fluctuations","volume":"41","author":"Jamroz","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2015.07.004_b0190","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1021\/ct300854w","article-title":"Consistent view of protein fluctuations from all-atom molecular dynamics and coarse-grained dynamics with knowledge-based force-field","volume":"9","author":"Jamroz","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/j.ymeth.2015.07.004_b0195","doi-asserted-by":"crossref","first-page":"2150","DOI":"10.1093\/bioinformatics\/btu184","article-title":"CABS-flex predictions of protein flexibility compared with NMR ensembles","volume":"30","author":"Jamroz","year":"2014","journal-title":"Bioinformatics"},{"issue":"W1","key":"10.1016\/j.ymeth.2015.07.004_b0200","doi-asserted-by":"crossref","first-page":"W306","DOI":"10.1093\/nar\/gkv359","article-title":"AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures","volume":"43","author":"Zambrano","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2015.07.004_b0205","doi-asserted-by":"crossref","first-page":"9443","DOI":"10.1073\/pnas.1015399108","article-title":"Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step","volume":"108","author":"Steczkiewicz","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ymeth.2015.07.004_b0210","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1007\/s00894-007-0177-8","article-title":"Hierarchical modeling of protein interactions","volume":"13","author":"Kurcinski","year":"2007","journal-title":"J. Mol. Model."},{"key":"10.1016\/j.ymeth.2015.07.004_b0215","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.jsbmb.2006.12.059","article-title":"Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators\u2019 sequences","volume":"103","author":"Kurcinski","year":"2007","journal-title":"J. Steroid Biochem. Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0220","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.jsbmb.2010.03.086","article-title":"Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid","volume":"121","author":"Kurcinski","year":"2010","journal-title":"J. Steroid Biochem. Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0225","first-page":"47","article-title":"Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2a","volume":"28","author":"Horwacik","year":"2011","journal-title":"Int. J. Mol. Med."},{"key":"10.1016\/j.ymeth.2015.07.004_b0230","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1021\/ct500287c","article-title":"Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations","volume":"10","author":"Kurcinski","year":"2014","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/j.ymeth.2015.07.004_b0235","first-page":"1","article-title":"Comparative protein structure modeling using MODELLER","volume":"2","author":"Eswar","year":"2007","journal-title":"Curr. Protoc. Protein Sci."},{"key":"10.1016\/j.ymeth.2015.07.004_b0240","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":"10.1016\/j.ymeth.2015.07.004_b0245","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1006\/jmbi.1997.1444","article-title":"Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH","volume":"274","author":"Katz","year":"1997","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0250","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1472-6807-7-43","article-title":"Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field","volume":"7","author":"Kmiecik","year":"2007","journal-title":"BMC Struct. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0255","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1002\/jcc.20624","article-title":"Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates","volume":"28","author":"Gront","year":"2007","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.ymeth.2015.07.004_b0260","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1002\/jcc.10314","article-title":"Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield","volume":"25","author":"Adcock","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.ymeth.2015.07.004_b0265","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1093\/protein\/2.5.335","article-title":"Modelling the polypeptide backbone with \u2018spare parts\u2019 from known protein structures","volume":"2","author":"Claessens","year":"1989","journal-title":"Protein Eng."},{"key":"10.1016\/j.ymeth.2015.07.004_b0270","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1002\/1097-0134(20001001)41:1<86::AID-PROT110>3.0.CO;2-Y","article-title":"Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models","volume":"41","author":"Feig","year":"2000","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0275","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/0022-2836(91)90883-8","article-title":"Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors","volume":"218","author":"Holm","year":"1991","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0280","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/0022-2836(92)90964-L","article-title":"Accurate modeling of protein conformation by automatic segment matching","volume":"226","author":"Levitt","year":"1992","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0285","doi-asserted-by":"crossref","first-page":"W147","DOI":"10.1093\/nar\/gkl289","article-title":"SABBAC: online structural alphabet-based protein backbone reconstruction from alpha-carbon trace","volume":"34","author":"Maupetit","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2015.07.004_b0290","doi-asserted-by":"crossref","first-page":"1881","DOI":"10.1002\/jcc.23330","article-title":"High-quality protein backbone reconstruction from alpha carbons using gaussian mixture models","volume":"34","author":"Moore","year":"2013","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.ymeth.2015.07.004_b0295","doi-asserted-by":"crossref","first-page":"2525","DOI":"10.1016\/j.bpj.2011.10.024","article-title":"Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization","volume":"101","author":"Xu","year":"2011","journal-title":"Biophys. J."},{"key":"10.1016\/j.ymeth.2015.07.004_b0300","doi-asserted-by":"crossref","first-page":"1832","DOI":"10.1038\/nprot.2008.184","article-title":"SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling","volume":"3","author":"Wang","year":"2008","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.ymeth.2015.07.004_b0305","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1002\/wcms.1090","article-title":"Optimization of protein models","volume":"2","author":"Gront","year":"2012","journal-title":"WIREs Comput. Mol. Sci."},{"key":"10.1016\/j.ymeth.2015.07.004_b0310","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1002\/prot.22380","article-title":"REMO: a new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks","volume":"76","author":"Li","year":"2009","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0315","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":"10.1016\/j.ymeth.2015.07.004_b0320","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1002\/prot.24428","article-title":"Docking, scoring, and affinity prediction in CAPRI","volume":"81","author":"Lensink","year":"2013","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0325","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nrd1549","article-title":"Docking and scoring in virtual screening for drug discovery: methods and applications","volume":"3","author":"Kitchen","year":"2004","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.ymeth.2015.07.004_b0330","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1023\/A:1011188704521","article-title":"Protein ligand docking based on empirical method for binding affinity estimation","volume":"15","author":"Tao","year":"2001","journal-title":"J. Comput. Aided Mol. Des."},{"key":"10.1016\/j.ymeth.2015.07.004_b0335","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1006\/jmbi.1999.3371","article-title":"Knowledge-based scoring function to predict protein\u2013ligand interactions","volume":"295","author":"Gohlke","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0340","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1002\/prot.20133","article-title":"Physical scoring function based on AMBER force field and Poisson\u2013Boltzmann implicit solvent for protein structure prediction","volume":"56","author":"Hsieh","year":"2004","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0345","doi-asserted-by":"crossref","first-page":"9304","DOI":"10.1021\/jp060334w","article-title":"Electrostatics of ligand binding: Parametrization of the generalized born model and comparison with the Poisson\u2013Boltzmann approach","volume":"110","author":"Liu","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"10.1016\/j.ymeth.2015.07.004_b0350","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1023\/A:1011115820450","article-title":"DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases","volume":"15","author":"Ewing","year":"2001","journal-title":"J. Comput. Aided Mol. Des."},{"key":"10.1016\/j.ymeth.2015.07.004_b0355","doi-asserted-by":"crossref","first-page":"6474","DOI":"10.1021\/jp003919d","article-title":"Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides","volume":"105","author":"Kaminski","year":"2001","journal-title":"J. Phys. Chem. B"},{"key":"10.1016\/j.ymeth.2015.07.004_b0360","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-atom empirical potential for molecular modeling and dynamics studies of proteins","volume":"102","author":"MacKerell","year":"1998","journal-title":"J. Phys. Chem. B"},{"key":"10.1016\/j.ymeth.2015.07.004_b0365","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","article-title":"Comparison of multiple amber force fields and development of improved protein backbone parameters","volume":"65","author":"Hornak","year":"2006","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0370","doi-asserted-by":"crossref","first-page":"3596","DOI":"10.1021\/jp984217f","article-title":"The GROMOS biomolecular simulation program package","volume":"103","author":"Scott","year":"1999","journal-title":"J. Phys. Chem. A"},{"key":"10.1016\/j.ymeth.2015.07.004_b0375","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/978-94-015-7658-1_21","article-title":"Interaction models for water in relation to protein hydration","volume":"14","author":"Berendsen","year":"1981","journal-title":"Intermolecular Forces"},{"key":"10.1016\/j.ymeth.2015.07.004_b0380","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.ymeth.2015.07.004_b0385","doi-asserted-by":"crossref","DOI":"10.1063\/1.3415372","article-title":"Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: insights from all-atom simulations","volume":"132","author":"Nam","year":"2010","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.ymeth.2015.07.004_b0390","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1016\/j.bpj.2012.03.024","article-title":"Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign","volume":"102","author":"Kuhrova","year":"2012","journal-title":"Biophys. J."},{"key":"10.1016\/j.ymeth.2015.07.004_b0395","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/j.ymeth.2015.07.004_b0400","doi-asserted-by":"crossref","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.ymeth.2015.07.004_b0405","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular-dynamics with coupling to an external bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.ymeth.2015.07.004_b0410","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald \u2013 an N. Log(N) method for Ewald Sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.ymeth.2015.07.004_b0415","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: a linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.ymeth.2015.07.004_b0420","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1002\/prot.22716","article-title":"Sub-angstrom modeling of complexes between flexible peptides and globular proteins","volume":"78","author":"Raveh","year":"2010","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0425","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1002\/prot.20831","article-title":"Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes","volume":"63","author":"Bordner","year":"2006","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0430","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1007\/978-1-4939-2020-4_12","article-title":"Mapping protein\u2013protein interactions with phage-displayed combinatorial peptide libraries and alanine scanning","volume":"1248","author":"Kokoszka","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0435","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1016\/j.cbpa.2013.10.011","article-title":"Druggable protein\u2013protein interactions \u2013 from hot spots to hot segments","volume":"17","author":"London","year":"2013","journal-title":"Curr. Opin. Chem. Biol."},{"key":"10.1016\/j.ymeth.2015.07.004_b0440","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/nature06526","article-title":"Reaching for high-hanging fruit in drug discovery at protein\u2013protein interfaces","volume":"450","author":"Wells","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.ymeth.2015.07.004_b0445","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1002\/prot.22785","article-title":"Can self-inhibitory peptides be derived from the interfaces of globular protein\u2013protein interactions?","volume":"78","author":"London","year":"2010","journal-title":"Proteins"},{"key":"10.1016\/j.ymeth.2015.07.004_b0450","unstructured":"E.O. Olmez, B.S. Akbulut, Protein\u2013Peptide Interactions Revolutionize Drug Development, 2012."},{"key":"10.1016\/j.ymeth.2015.07.004_b0455","doi-asserted-by":"crossref","first-page":"3244","DOI":"10.1093\/bioinformatics\/btm493","article-title":"Pepitope: epitope mapping from affinity-selected peptides","volume":"23","author":"Mayrose","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ymeth.2015.07.004_b0460","series-title":"Development of antibody-based therapeutics: translational considerations","author":"Tabrizi","year":"2012"},{"key":"10.1016\/j.ymeth.2015.07.004_b0465","doi-asserted-by":"crossref","first-page":"145","DOI":"10.2165\/00063030-200721030-00002","article-title":"Epitope mapping: the first step in developing epitope-based vaccines","volume":"21","author":"Gershoni","year":"2007","journal-title":"BioDrugs"}],"container-title":["Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1046202315300207?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1046202315300207?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2020,9,4]],"date-time":"2020-09-04T21:56:56Z","timestamp":1599256616000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1046202315300207"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1]]},"references-count":93,"alternative-id":["S1046202315300207"],"URL":"https:\/\/doi.org\/10.1016\/j.ymeth.2015.07.004","relation":{},"ISSN":["1046-2023"],"issn-type":[{"value":"1046-2023","type":"print"}],"subject":[],"published":{"date-parts":[[2016,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Modeling of protein\u2013peptide interactions using the CABS-dock web server for binding site search and flexible docking","name":"articletitle","label":"Article Title"},{"value":"Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ymeth.2015.07.004","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2016 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}