{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T21:46:38Z","timestamp":1781819198147,"version":"3.54.5"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2018,3,15]],"date-time":"2018-03-15T00:00:00Z","timestamp":1521072000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-11-MONU-006-01"],"award-info":[{"award-number":["ANR-11-MONU-006-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["16-14-10273"],"award-info":[{"award-number":["16-14-10273"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"name":"President of the Russian Federation","award":["MK-5279.2018.4"],"award-info":[{"award-number":["MK-5279.2018.4"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The root mean square deviation (RMSD) is one of the most used similarity criteria in structural biology and bioinformatics. Standard computation of the RMSD has a linear complexity with respect to the number of atoms in a molecule, making RMSD calculations time-consuming for the large-scale modeling applications, such as assessment of molecular docking predictions or clustering of spatially proximate molecular conformations. Previously, we introduced the RigidRMSD algorithm to compute the RMSD corresponding to the rigid-body motion of a molecule. In this study, we go beyond the limits of the rigid-body approximation by taking into account conformational flexibility of the molecule. We model the flexibility with a reduced set of collective motions computed with e.g. normal modes or principal component analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The initialization of our algorithm is linear in the number of atoms and all the subsequent evaluations of RMSD values between flexible molecular conformations depend only on the number of collective motions that are selected to model the flexibility. Therefore, our algorithm is much faster compared to the standard RMSD computation for large-scale modeling applications. We demonstrate the efficiency of our method on several clustering examples, including clustering of flexible docking results and molecular dynamics (MD) trajectories. We also demonstrate how to use the presented formalism to generate pseudo-random constant-RMSD structural molecular ensembles and how to use these in cross-docking.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>We provide the algorithm written in C++ as the open-source RapidRMSD library governed by the BSD-compatible license, which is available at http:\/\/team.inria.fr\/nano-d\/software\/RapidRMSD\/. The constant-RMSD structural ensemble application and clustering of MD trajectories is available at http:\/\/team.inria.fr\/nano-d\/software\/nolb-normal-modes\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty160","type":"journal-article","created":{"date-parts":[[2018,3,15]],"date-time":"2018-03-15T10:02:55Z","timestamp":1521108175000},"page":"2757-2765","source":"Crossref","is-referenced-by-count":31,"title":["RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules"],"prefix":"10.1093","volume":"34","author":[{"given":"Emilie","family":"Neveu","sequence":"first","affiliation":[{"name":"Inria\/Univ. Grenoble Alpes\/LJK-CNRS, Grenoble, France"},{"name":"Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petr","family":"Popov","sequence":"additional","affiliation":[{"name":"Inria\/Univ. Grenoble Alpes\/LJK-CNRS, Grenoble, France"},{"name":"Moscow Institute of Physics and Technology, Dolgoprudniy, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre","family":"Hoffmann","sequence":"additional","affiliation":[{"name":"Inria\/Univ. Grenoble Alpes\/LJK-CNRS, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angelo","family":"Migliosi","sequence":"additional","affiliation":[{"name":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Besseron","sequence":"additional","affiliation":[{"name":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gr\u00e9goire","family":"Danoy","sequence":"additional","affiliation":[{"name":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascal","family":"Bouvry","sequence":"additional","affiliation":[{"name":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1903-7220","authenticated-orcid":false,"given":"Sergei","family":"Grudinin","sequence":"additional","affiliation":[{"name":"Inria\/Univ. Grenoble Alpes\/LJK-CNRS, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,3,15]]},"reference":[{"key":"2023012712583062900_bty160-B1","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S1359-0278(97)00024-2","article-title":"Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential","volume":"2","author":"Bahar","year":"1997","journal-title":"Folding Des"},{"key":"2023012712583062900_bty160-B2","doi-asserted-by":"crossref","first-page":"6571","DOI":"10.1073\/pnas.80.21.6571","article-title":"Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc","volume":"80","author":"Brooks","year":"1983","journal-title":"Natl Acad. Sci. U.S.A"},{"key":"2023012712583062900_bty160-B3","doi-asserted-by":"crossref","first-page":"9632","DOI":"10.1021\/ja042260c","article-title":"Representing receptor flexibility in ligand docking through relevant normal modes","volume":"127","author":"Cavasotto","year":"2005","journal-title":"J. Am. Chem. Soc"},{"key":"2023012712583062900_bty160-B4","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1002\/prot.10389","article-title":"ZDOCK: an initial-stage protein-docking algorithm","volume":"52","author":"Chen","year":"2003","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B5","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.jsb.2005.03.006","article-title":"Predicting oligomeric assemblies: n-mers a primer","volume":"150","author":"Comeau","year":"2005","journal-title":"J. Struct. Biol"},{"key":"2023012712583062900_bty160-B6","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1002\/jcc.20110","article-title":"Using quaternions to calculate RMSD","volume":"25","author":"Coutsias","year":"2004","journal-title":"J. Comput. Chem"},{"key":"2023012712583062900_bty160-B7","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1109\/4235.996017","article-title":"A fast and elitist multiobjective genetic algorithm: nSGA-II","volume":"6","author":"Deb","year":"2002","journal-title":"IEEE Trans. Evol. Comput"},{"key":"2023012712583062900_bty160-B8","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1107\/S0108767387010535","article-title":"A note on the rotational superposition problem","volume":"44","author":"Diamond","year":"1988","journal-title":"Acta Crystallogr., Sect. A: Found. Crystallogr"},{"key":"2023012712583062900_bty160-B9","doi-asserted-by":"crossref","first-page":"10390","DOI":"10.1073\/pnas.0802496105","article-title":"Insights into protein flexibility: the relationship between normal modes and conformational change upon protein\u2013protein docking","volume":"105","author":"Dobbins","year":"2008","journal-title":"Proc. Natl Acad. Sci. U.S.A"},{"key":"2023012712583062900_bty160-B10","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"Haddock: a protein-protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J. Am. Chem. Soc"},{"key":"2023012712583062900_bty160-B11","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1002\/prot.21613","article-title":"Hingeprot: automated prediction of hinges in protein structures","volume":"70","author":"Emekli","year":"2008","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B12","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1002\/prot.22808","article-title":"Binding site prediction and improved scoring during flexible protein\u2013protein docking with attract","volume":"78","author":"Fiorucci","year":"2010","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B13","doi-asserted-by":"crossref","first-page":"3236","DOI":"10.1021\/ct500306s","article-title":"pyproct: automated cluster analysis for structural bioinformatics","volume":"10","author":"Gil","year":"2014","journal-title":"J. Chem. Theory Comput"},{"key":"2023012712583062900_bty160-B14","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1016\/j.str.2004.09.014","article-title":"Complementarity of structure ensembles in protein-protein binding","volume":"12","author":"Gr\u00fcnberg","year":"2004","journal-title":"Structure"},{"key":"2023012712583062900_bty160-B15","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1093\/proeng\/gzg021","article-title":"Effect of local shape modifications of molecular surfaces on rigid-body protein\u2013protein docking","volume":"16","author":"Heifetz","year":"2003","journal-title":"Protein Eng"},{"key":"2023012712583062900_bty160-B16","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1002\/jcc.23513","article-title":"Efficient computation of root mean square deviations under rigid transformations","volume":"35","author":"Hildebrandt","year":"2014","journal-title":"J. Comput. Chem"},{"key":"2023012712583062900_bty160-B17","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1002\/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8","article-title":"Analysis of domain motions by approximate normalmode calculations","volume":"33","author":"Hinsen","year":"1998","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B18","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1002\/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B","article-title":"The molecular modeling toolkit: a new approach to molecular simulations","volume":"21","author":"Hinsen","year":"2000","journal-title":"J. Comput. Chem"},{"key":"2023012712583062900_bty160-B19","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1021\/acs.jctc.7b00197","article-title":"NOLB: nonlinear rigid block normal-mode analysis method","volume":"13","author":"Hoffmann","year":"2017","journal-title":"J. Chem. Theory Comput"},{"key":"2023012712583062900_bty160-B20","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","article-title":"Protein structure comparison by alignment of distance matrices","volume":"233","author":"Holm","year":"1993","journal-title":"J. Mol. Biol"},{"key":"2023012712583062900_bty160-B21","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1364\/JOSAA.4.000629","article-title":"Closed-form solution of absolute orientation using unit quaternions","volume":"4","author":"Horn","year":"1987","journal-title":"J. Opt. Soc. Am. A"},{"key":"2023012712583062900_bty160-B22","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1016\/j.drudis.2014.02.005","article-title":"Search strategies and evaluation in protein\u2013protein docking: principles, advances and challenges","volume":"19","author":"Huang","year":"2014","journal-title":"Drug Disc. Today"},{"key":"2023012712583062900_bty160-B23","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.1093\/bioinformatics\/btu098","article-title":"fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data","volume":"30","author":"Hung","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012712583062900_bty160-B24","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1110\/ps.041081905","article-title":"Assessing predictions of protein\u2013protein interaction: the CAPRI experiment","volume":"14","author":"Janin","year":"2005","journal-title":"Protein Sci"},{"key":"2023012712583062900_bty160-B25","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1107\/S0108767388010128","article-title":"On the orthogonal transformation used for structural comparisons","volume":"45","author":"Kearsley","year":"1989","journal-title":"Acta Crystallogr., Sect. A: Found. Crystallogr"},{"key":"2023012712583062900_bty160-B26","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1080\/08927029108022453","article-title":"Superposition of molecular structures using quaternions","volume":"7","author":"Kneller","year":"1991","journal-title":"Mol. Simul"},{"key":"2023012712583062900_bty160-B27","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1002\/prot.20151","article-title":"Predictions of protein flexibility: first-order measures","volume":"56","author":"Kovacs","year":"2004","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B28","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1529\/biophysj.104.058768","article-title":"Optimal clustering for detecting near-native conformations in protein docking","volume":"89","author":"Kozakov","year":"2005","journal-title":"Biophys. J"},{"key":"2023012712583062900_bty160-B29","doi-asserted-by":"crossref","first-page":"4496","DOI":"10.1093\/nar\/gki730","article-title":"Refinement of docked protein\u2013ligand and protein\u2013DNA structures using low frequency normal mode amplitude optimization","volume":"33","author":"Lindahl","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023012712583062900_bty160-B30","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/prot.21442","article-title":"Identification of near-native structures by clustering protein docking conformations","volume":"68","author":"Lorenzen","year":"2007","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B31","doi-asserted-by":"crossref","first-page":"W358","DOI":"10.1093\/nar\/gkt383","article-title":"T-rmsd: a web server for automated fine-grained protein structural classification","volume":"41","author":"Magis","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012712583062900_bty160-B32","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1002\/prot.22668","article-title":"Fiberdock: flexible induced-fit backbone refinement in molecular docking","volume":"78","author":"Maschiach","year":"2010","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B33","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1002\/prot.21579","article-title":"Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein\u2013protein docking","volume":"70","author":"May","year":"2007","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B34","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":"M\u00e9ndez","year":"2003","journal-title":"Proteins: Struct., Funct., Genet"},{"key":"2023012712583062900_bty160-B35","doi-asserted-by":"crossref","first-page":"3623","DOI":"10.3390\/ijms11103623","article-title":"Swarmdock and the use of normal modes in protein-protein docking","volume":"11","author":"Moal","year":"2010","journal-title":"Int. J. Mol. Sci"},{"key":"2023012712583062900_bty160-B36","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1002\/prot.20569","article-title":"Docking essential dynamics eigenstructures","volume":"60","author":"Mustard","year":"2005","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B37","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1002\/(SICI)1097-0134(20000601)39:4<372::AID-PROT100>3.0.CO;2-Q","article-title":"BiGGER: A new (soft) docking algorithm for predicting protein interactions","volume":"39","author":"Palma","year":"2000","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B38","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1002\/jcc.23569","article-title":"Rapid determination of rmsds corresponding to macromolecular rigid body motions","volume":"35","author":"Popov","year":"2014","journal-title":"J. Comput. Chem"},{"key":"2023012712583062900_bty160-B39","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1021\/acs.jcim.5b00372","article-title":"Knowledge of native protein-protein interfaces is sufficient to construct predictive models for the selection of binding candidates","volume":"55","author":"Popov","year":"2015","journal-title":"J. Chem. Inf. Model"},{"key":"2023012712583062900_bty160-B40","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1002\/prot.24344","article-title":"Docktrina: docking triangular protein trimers","volume":"82","author":"Popov","year":"2014","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B41","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.jmgm.2018.01.015","article-title":"Eurecon: equidistant uniform rigid-body ensemble constructor","volume":"80","author":"Popov","year":"2018","journal-title":"J. Mol. Graphics Model"},{"key":"2023012712583062900_bty160-B42","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1002\/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6","article-title":"Protein docking using spherical polar fourier correlations","volume":"39","author":"Ritchie","year":"2000","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B43","doi-asserted-by":"crossref","first-page":"3309","DOI":"10.1021\/acs.jpclett.5b01456","article-title":"Machine learning for quantum mechanical properties of atoms in molecules","volume":"6","author":"Rupp","year":"2015","journal-title":"J. Phys. Chem. Lett"},{"key":"2023012712583062900_bty160-B44","doi-asserted-by":"crossref","first-page":"12.","DOI":"10.1186\/1748-7188-5-12","article-title":"Flexsnap: flexible non-sequential protein structure alignment","volume":"5","author":"Salem","year":"2010","journal-title":"Algorithms Mol. Biol"},{"key":"2023012712583062900_bty160-B45","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1002\/prot.21759","article-title":"Automatic prediction of protein interactions with large scale motion","volume":"69","author":"Schneidman-Duhovny","year":"2007","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B46","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1002\/prot.10100","article-title":"Flexible protein alignment and hinge detection","volume":"48","author":"Shatsky","year":"2002","journal-title":"Proteins: Struct., Funct., Genet"},{"key":"2023012712583062900_bty160-B47","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1002\/prot.10628","article-title":"A method for simultaneous alignment of multiple protein structures","volume":"56","author":"Shatsky","year":"2004","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B48","doi-asserted-by":"crossref","first-page":"3192","DOI":"10.1039\/C6SC05720A","article-title":"ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost","volume":"8","author":"Smith","year":"2017","journal-title":"Chem. Sci"},{"key":"2023012712583062900_bty160-B49","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/1097-0134(20001001)41:1<1::AID-PROT10>3.0.CO;2-P","article-title":"Building-block approach for determining low-frequency normal modes of macromolecules","volume":"41","author":"Tama","year":"2000","journal-title":"Proteins: Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B50","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1107\/S0108767305015266","article-title":"Rapid calculation of RMSDs using a quaternion-based characteristic polynomial","volume":"61","author":"Theobald","year":"2005","journal-title":"Acta Crystallogr., Sect. A: Found. Crystallogr"},{"key":"2023012712583062900_bty160-B51","doi-asserted-by":"crossref","first-page":"1905.","DOI":"10.1103\/PhysRevLett.77.1905","article-title":"Large amplitude elastic motions in proteins from a single-parameter, atomic analysis","volume":"77","author":"Tirion","year":"1996","journal-title":"Phys. Rev. Lett"},{"key":"2023012712583062900_bty160-B52","doi-asserted-by":"crossref","first-page":"2262","DOI":"10.1002\/prot.24115","article-title":"Flexible protein docking refinement using pose-dependent normal mode analysis","volume":"80","author":"Venkatraman","year":"2012","journal-title":"Proteins: Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B53","doi-asserted-by":"crossref","first-page":"3031","DOI":"10.1016\/j.jmb.2015.07.016","article-title":"Updates to the integrated protein\u2013protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2","volume":"427","author":"Vreven","year":"2015","journal-title":"J. Mol. Biol"},{"key":"2023012712583062900_bty160-B54","volume-title":"Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra","author":"Wilson","year":"1955"},{"key":"2023012712583062900_bty160-B55","doi-asserted-by":"crossref","first-page":"ii246","DOI":"10.1093\/bioinformatics\/btg1086","article-title":"Flexible structure alignment by chaining aligned fragment pairs allowing twists","volume":"19","author":"Ye","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012712583062900_bty160-B56","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/j.sbi.2010.02.001","article-title":"Accounting for conformational changes during protein\u2013protein docking","volume":"20","author":"Zacharias","year":"2010","journal-title":"Curr. Opin. Struct. Biol"},{"key":"2023012712583062900_bty160-B57","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/prot.20179","article-title":"Modeling correlated main-chain motions in proteins for flexible molecular recognition","volume":"57","author":"Zavodszky","year":"2004","journal-title":"Proteins: Struct. Funct. Bioinf"},{"key":"2023012712583062900_bty160-B58","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1002\/jcc.20011","article-title":"Spicker: a clustering approach to identify near-native protein folds","volume":"25","author":"Zhang","year":"2004","journal-title":"J. Comput. Chem"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/16\/2757\/48917298\/bioinformatics_34_16_2757.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/16\/2757\/48917298\/bioinformatics_34_16_2757.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:47:02Z","timestamp":1674827222000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/16\/2757\/4938487"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,3,15]]},"references-count":58,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2018,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty160","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,8,15]]},"published":{"date-parts":[[2018,3,15]]}}}