{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T04:09:31Z","timestamp":1789877371541,"version":"4.0.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Modeling of side chain conformations constitutes an indispensable effort in protein structure modeling, protein\u2013protein docking and protein design. Thanks to an intensive attention to this field, many of the existing programs can achieve reasonably good and comparable prediction accuracy. Moreover, in our previous work on CIS-RR, we argued that the prediction with few atomic clashes can complement the current existing methods for subsequent analysis and refinement of protein structures. However, these recent efforts to enhance the quality of predicted side chains have been accompanied by a significant increase of computational cost.<\/jats:p>\n               <jats:p>Results: In this study, by mainly focusing on improving the speed of side chain conformation prediction, we present a RApid Side-chain Predictor, called RASP. To achieve a much faster speed with a comparable accuracy to the best existing methods, we not only employ the clash elimination strategy of CIS-RR, but also carefully optimize energy terms and integrate different search algorithms. In comprehensive benchmark testings, RASP is over one order of magnitude faster (~ 40 times over CIS-RR) than the recently developed methods, while achieving comparable or even better accuracy.<\/jats:p>\n               <jats:p>Availability: RASP is available to non-commercial users at our website: http:\/\/jianglab.ibp.ac.cn\/lims\/rasp\/rasp<\/jats:p>\n               <jats:p>Contact: \u00a0taijiao@moon.ibp.ac.cn<\/jats:p>\n               <jats:p>Supplementary Information: Supplementary information is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr538","type":"journal-article","created":{"date-parts":[[2011,9,25]],"date-time":"2011-09-25T00:18:39Z","timestamp":1316909919000},"page":"3117-3122","source":"Crossref","is-referenced-by-count":59,"title":["RASP: rapid modeling of protein side chain conformations"],"prefix":"10.1093","volume":"27","author":[{"given":"Zhichao","family":"Miao","sequence":"first","affiliation":[{"name":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"},{"name":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Cao","sequence":"additional","affiliation":[{"name":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"},{"name":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taijiao","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,9,23]]},"reference":[{"key":"2023012511320921700_B1","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1006\/jmbi.1997.0926","article-title":"Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool","volume":"267","author":"Bower","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B2","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":"Brooks","year":"1983","journal-title":"J. Comput. Chem."},{"key":"2023012511320921700_B3","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1110\/ps.03154503","article-title":"A graph-theory algorithm for rapid protein side-chain prediction","volume":"12","author":"Canutescu","year":"2003","journal-title":"Protein Sci."},{"key":"2023012511320921700_B4","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1002\/pro.5560050511","article-title":"Protein design automation","volume":"5","author":"Dahiyat","year":"1996","journal-title":"Protein Sci."},{"key":"2023012511320921700_B5","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/S1359-0278(97)00006-0","article-title":"All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination","volume":"2","author":"DeMaeyer","year":"1997","journal-title":"Fold Des."},{"key":"2023012511320921700_B6","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/356539a0","article-title":"The dead-end elimination theorem and its use in protein side-chain positioning","volume":"356","author":"Desmet","year":"1992","journal-title":"Nature"},{"key":"2023012511320921700_B7","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/S0959-440X(02)00344-5","article-title":"Rotamer libraries in the 21(st) century","volume":"12","author":"Dunbrack","year":"2002","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023012511320921700_B8","doi-asserted-by":"crossref","first-page":"1661","DOI":"10.1002\/pro.5560060807","article-title":"Bayesian statistical analysis of protein side-chain rotamer preferences","volume":"6","author":"Dunbrack","year":"1997","journal-title":"Protein Sci."},{"key":"2023012511320921700_B9","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1006\/jmbi.1993.1170","article-title":"Backbone-dependent rotamer library for proteins - application to side-chain prediction","volume":"230","author":"Dunbrack","year":"1993","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B10","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1107\/S0108767391001071","article-title":"Accurate Bond and Angle Parameters for X-Ray Protein-Structure Refinement","volume":"47","author":"Engh","year":"1991","journal-title":"Acta Crystallogr. A"},{"key":"2023012511320921700_B11","doi-asserted-by":"crossref","first-page":"2030","DOI":"10.1110\/ps.072855507","article-title":"Modeling mutations in protein structures","volume":"16","author":"Feyfant","year":"2007","journal-title":"Protein Sci."},{"key":"2023012511320921700_B12","doi-asserted-by":"crossref","first-page":"2466","DOI":"10.1093\/bioinformatics\/btq445","article-title":"SPRINT: side-chain prediction inference toolbox for multistate protein design","volume":"26","author":"Fromer","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012511320921700_B13","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1016\/S0006-3495(94)80923-3","article-title":"Efficient Rotamer Elimination Applied to Protein Side-Chains and Related Spin-Glasses","volume":"66","author":"Goldstein","year":"1994","journal-title":"Biophys. J."},{"key":"2023012511320921700_B14","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/S0969-2126(99)80176-2","article-title":"Branch-and-terminate: a combinatorial optimization algorithm for protein design","volume":"7","author":"Gordon","year":"1999","journal-title":"Structure"},{"key":"2023012511320921700_B15","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0022-2836(03)00670-3","article-title":"Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations","volume":"331","author":"Gray","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B16","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-11-306","article-title":"Beyond rotamers: a generative, probabilistic model of side chains in proteins","volume-title":"BMC Bioinformatics","author":"Harder","year":"2010"},{"key":"2023012511320921700_B17","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1110\/ps.062658307","article-title":"IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models","volume":"16","author":"Hartmann","year":"2007","journal-title":"Protein Sci."},{"key":"2023012511320921700_B18","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 Coordinates from a C-Alpha Trace Application to Model-Building and Detection of Coordinate Errors","volume":"218","author":"Holm","year":"1991","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B19","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/S0022-2836(02)00470-9","article-title":"On the role of the crystal environment in determining protein side-chain conformations","volume":"320","author":"Jacobson","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B20","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1110\/ps.062165906","article-title":"Configurational-bias sampling technique for predicting side-chain conformations in proteins","volume":"15","author":"Jain","year":"2006","journal-title":"Protein Sci."},{"key":"2023012511320921700_B21","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1002\/pro.5560030405","article-title":"De-novo protein design using pairwise potentials and a genetic algorithm","volume":"3","author":"Jones","year":"1994","journal-title":"Protein Sci."},{"key":"2023012511320921700_B22","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1093\/bioinformatics\/btr009","article-title":"Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation","volume":"27","author":"Jiang","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012511320921700_B23","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1093\/bioinformatics\/bti144","article-title":"Solving and analyzing side-chain positioning problems using linear and integer programming","volume":"21","author":"Kingsford","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012511320921700_B24","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1002\/prot.22488","article-title":"Improved prediction of protein side-chain conformations with SCWRL4","volume":"77","author":"Krivov","year":"2009","journal-title":"Proteins"},{"key":"2023012511320921700_B25","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1002\/(SICI)1097-0134(19981101)33:2<227::AID-PROT7>3.0.CO;2-F","article-title":"Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm","volume":"33","author":"Leach","year":"1998","journal-title":"Proteins Struct. Funct. Genet."},{"key":"2023012511320921700_B26","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1006\/jmbi.1994.1198","article-title":"Predicting protein mutant energetics by self-consistent ensemble optimization","volume":"236","author":"Lee","year":"1994","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B27","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/0022-2836(91)90550-P","article-title":"Prediction of protein side-chain conformation by packing optimization","volume":"217","author":"Lee","year":"1991","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B28","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1110\/ps.24902","article-title":"Side-chain modeling with an optimized scoring function","volume":"11","author":"Liang","year":"2002","journal-title":"Protein Sci."},{"key":"2023012511320921700_B29","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1002\/jcc.21747","article-title":"Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions","volume":"32","author":"Liang","year":"2011","journal-title":"J. Comput. Chem."},{"key":"2023012511320921700_B30","volume-title":"Monte Carlo Strategies in Scientific Computing","author":"Liu","year":"2008","edition":"1st"},{"key":"2023012511320921700_B31","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.jmb.2007.11.033","article-title":"OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing","volume":"376","author":"Lu","year":"2008","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B32","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1110\/ps.035022.108","article-title":"OPUS-Rota: A fast and accurate method for side-chain modeling","volume":"17","author":"Lu","year":"2008","journal-title":"Protein Sci."},{"key":"2023012511320921700_B33","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/0022-2836(87)90314-7","article-title":"Analysis of the relationship between side-chain conformation and secondary structure in globular-proteins","volume":"198","author":"Mcgregor","year":"1987","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B34","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1002\/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H","article-title":"Improved modeling of side-chains in proteins with rotamer-based methods: a flexible rotamer model","volume":"37","author":"Mendes","year":"1999","journal-title":"Proteins Struct. Funct. Genet."},{"key":"2023012511320921700_B35","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1023\/A:1012279810260","article-title":"Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants","volume":"15","author":"Mendes","year":"2001","journal-title":"J. Comput. Aid. Mol. Des."},{"key":"2023012511320921700_B36","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1002\/jcc.20237","article-title":"Practical conversion from torsion space to Cartesian space for in silico protein synthesis","volume":"26","author":"Parsons","year":"2005","journal-title":"J. Comput. Chem."},{"key":"2023012511320921700_B37","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1110\/ps.03250104","article-title":"Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library","volume":"13","author":"Peterson","year":"2004","journal-title":"Protein Sci."},{"key":"2023012511320921700_B38","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/0022-2836(87)90358-5","article-title":"Tertiary templates for proteins - use of packing criteria in the enumeration of allowed sequences for different structural classes","volume":"193","author":"Ponder","year":"1987","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B39","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0076-6879(04)83004-0","article-title":"Protein structure prediction using rosetta","volume":"383","author":"Rohl","year":"2004","journal-title":"Method Enzymol."},{"key":"2023012511320921700_B40","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1006\/jmbi.1998.1689","article-title":"A graph-theoretic algorithm for comparative modeling of protein structure","volume":"279","author":"Samudrala","year":"1998","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B41","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1016\/j.str.2011.03.019","article-title":"A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions","volume":"19","author":"Shapovalov","year":"2011","journal-title":"Structure"},{"key":"2023012511320921700_B42","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1137\/0201010","article-title":"Depth-first search and linear graph algorithms","volume":"1","author":"Tarjan","year":"1972","journal-title":"SIAM J. Comput."},{"key":"2023012511320921700_B43","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1080\/07391102.1991.10507882","article-title":"A new approach to the rapid-determination of protein side-chain conformations","volume":"8","author":"Tuffery","year":"1991","journal-title":"J. Biomol. Struct. Dyn."},{"key":"2023012511320921700_B44","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1002\/bip.360360106","article-title":"An evaluation of discrete and continuum search techniques for conformational-analysis of side-chains in proteins","volume":"36","author":"Vasquez","year":"1995","journal-title":"Biopolymers"},{"key":"2023012511320921700_B45","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","article-title":"PISCES: a protein sequence culling server","volume":"19","author":"Wang","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012511320921700_B46","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1006\/jmbi.2001.4985","article-title":"Extending the accuracy limits of prediction for side-chain conformations (vol 311, pg 421, 2001)","volume":"312","author":"Xiang","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012511320921700_B47","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/11415770_32","article-title":"Rapid protein side-chain packing via tree decomposition","volume":"3500","author":"Xu","year":"2005","journal-title":"Lect. Notes Comput. Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/22\/3117\/48862399\/bioinformatics_27_22_3117.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/22\/3117\/48862399\/bioinformatics_27_22_3117.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:33:27Z","timestamp":1674646407000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/22\/3117\/195223"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,9,23]]},"references-count":47,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2011,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr538","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,11,15]]},"published":{"date-parts":[[2011,9,23]]}}}