{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T13:03:38Z","timestamp":1725455018611},"publisher-location":"Berlin, Heidelberg","reference-count":28,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642331213"},{"type":"electronic","value":"9783642331220"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-642-33122-0_21","type":"book-chapter","created":{"date-parts":[[2012,8,28]],"date-time":"2012-08-28T10:43:09Z","timestamp":1346150589000},"page":"262-273","source":"Crossref","is-referenced-by-count":0,"title":["MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing"],"prefix":"10.1007","author":[{"given":"Natalie E.","family":"Castellana","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrey","family":"Lushnikov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Piotr","family":"Rotkiewicz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natasha","family":"Sefcovic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pavel A.","family":"Pevzner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Godzik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kira","family":"Vyatkina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"1","key":"21_CR1","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"H.M. Berman","year":"2000","unstructured":"Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Research\u00a028(1), 235\u2013242 (2000)","journal-title":"Nucleic Acids Research"},{"key":"21_CR2","doi-asserted-by":"crossref","unstructured":"Echols, N., Milburn, D., Gerstein, M.: Molmovdb: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Research, 478\u2013482 (2003)","DOI":"10.1093\/nar\/gkg104"},{"key":"21_CR3","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.1016\/S0006-3495(02)73931-3","volume":"83","author":"M.K. Kim","year":"2002","unstructured":"Kim, M.K., Jernigan, R.L., Chirikjian, G.S.: Efficient generation of feasible pathways for protein conformational transitions. Biophys. J.\u00a083, 1620\u20131630 (2002)","journal-title":"Biophys. J."},{"key":"21_CR4","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/S1093-3263(02)00143-2","volume":"21","author":"M.K. Kim","year":"2002","unstructured":"Kim, M.K., Chirikjian, G.S., Jernigan, R.L.: Elastic models of conformational transitions in macromolecules. J. Mol. Graph. Model.\u00a021, 151\u2013160 (2002)","journal-title":"J. Mol. Graph. Model."},{"key":"21_CR5","doi-asserted-by":"crossref","unstructured":"Franklin, J., Koehl, P., Doniach, S., Delarue, M.: Minactionpath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Research, 477\u2013482 (2007)","DOI":"10.1093\/nar\/gkm342"},{"key":"21_CR6","doi-asserted-by":"publisher","first-page":"1038","DOI":"10.1002\/prot.20907","volume":"63","author":"A. Ahmed","year":"2006","unstructured":"Ahmed, A., Gohlke, H.: Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins\u00a063, 1038\u20131051 (2006)","journal-title":"Proteins"},{"key":"21_CR7","doi-asserted-by":"publisher","first-page":"920","DOI":"10.1529\/biophysj.106.095927","volume":"93","author":"L. Yang","year":"2007","unstructured":"Yang, L., Song, G., Jernigan, R.L.: How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys. J.\u00a093, 920\u2013929 (2007)","journal-title":"Biophys. J."},{"key":"21_CR8","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1093\/nar\/28.8.1665","volume":"28","author":"W.G. Krebs","year":"2000","unstructured":"Krebs, W.G., Gerstein, M.: The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res.\u00a028, 1665\u20131675 (2000)","journal-title":"Nucleic Acids Res."},{"issue":"5389","key":"21_CR9","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1126\/science.282.5389.740","volume":"282","author":"Y. Duan","year":"1998","unstructured":"Duan, Y., Kollman, P.A.: Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science\u00a0282(5389), 740\u2013744 (1998)","journal-title":"Science"},{"issue":"2","key":"21_CR10","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1089\/10665270252935395","volume":"9","author":"N.M. Amato","year":"2002","unstructured":"Amato, N.M., Song, G.: Using motion planning to study protein folding pathways. Journal of Computational Biology\u00a09(2), 149\u2013168 (2002)","journal-title":"Journal of Computational Biology"},{"issue":"3-4","key":"21_CR11","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1089\/10665270360688011","volume":"10","author":"M.S. Apaydin","year":"2003","unstructured":"Apaydin, M.S., Brutlag, D.L., Guestrin, C., Hsu, D., Latombe, J.C., Varma, C.: Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. Journal of Computational Biology\u00a010(3-4), 257\u2013281 (2003)","journal-title":"Journal of Computational Biology"},{"key":"21_CR12","doi-asserted-by":"crossref","unstructured":"Raveh, B., Enosh, A., Schueler-Furman, O., Halperin, D.: Rapid sampling of molecular motions with prior information constraints. PLoS Comput. Biol.\u00a05(2), e1000295 (2009)","DOI":"10.1371\/journal.pcbi.1000295"},{"key":"21_CR13","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.2174\/1381612033454595","volume":"9","author":"M.L. Teodoro","year":"2003","unstructured":"Teodoro, M.L., Kavraki, L.E.: Conformational flexibility models for the receptor in structure based drug design. Curr. Pharm. Des.\u00a09, 1635\u20131648 (2003)","journal-title":"Curr. Pharm. Des."},{"key":"21_CR14","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/S1367-5931(02)00341-1","volume":"6","author":"H.A. Carlson","year":"2002","unstructured":"Carlson, H.A.: Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol.\u00a06, 447\u2013452 (2002)","journal-title":"Curr. Opin. Chem. Biol."},{"key":"21_CR15","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1006\/jmbi.1996.0776","volume":"266","author":"R.M. Knegtel","year":"1997","unstructured":"Knegtel, R.M., Kuntz, I.D., Oshiro, C.M.: Molecular docking to ensembles of protein structures. J. Mol. Biol.\u00a0266, 424\u2013440 (1997)","journal-title":"J. Mol. Biol."},{"key":"21_CR16","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1021\/ci900407c","volume":"50","author":"I.R. Craig","year":"2010","unstructured":"Craig, I.R., Essex, J.W., Spiegel, K.: Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments. J. Chem. Inf. Model\u00a050, 511\u2013524 (2010)","journal-title":"J. Chem. Inf. Model"},{"issue":"1","key":"21_CR17","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.sbi.2004.01.005","volume":"14","author":"C.S. Goh","year":"2004","unstructured":"Goh, C.S., Milburn, D., Gerstein, M.: Conformational changes associated with protein-protein interactions. Current Opinion in Structural Biology\u00a014(1), 104\u2013109 (2004)","journal-title":"Current Opinion in Structural Biology"},{"issue":"6","key":"21_CR18","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1111\/j.1399-3011.1975.tb02465.x","volume":"7","author":"H. Taketomi","year":"1975","unstructured":"Taketomi, H., Ueda, Y., Go, N.: Studies on protein folding, unfolding and fluctuations by computer simulation. International Journal of Peptide and Protein Research\u00a07(6), 445\u2013459 (1975)","journal-title":"International Journal of Peptide and Protein Research"},{"issue":"10","key":"21_CR19","doi-asserted-by":"publisher","first-page":"3986","DOI":"10.1021\/ma00200a030","volume":"22","author":"K.F. Lau","year":"1989","unstructured":"Lau, K.F., Dill, K.A.: A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules\u00a022(10), 3986\u20133997 (1989)","journal-title":"Macromolecules"},{"key":"21_CR20","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1038\/369248a0","volume":"369","author":"A. Sali","year":"1994","unstructured":"Sali, A., Shakhnovich, E., Karplus, M.: How does a protein fold? Nature\u00a0369, 248\u2013251 (1994)","journal-title":"Nature"},{"key":"21_CR21","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1016\/j.jmb.2008.10.064","volume":"385","author":"D.R. Weiss","year":"2009","unstructured":"Weiss, D.R., Levitt, M.: Can morphing methods predict intermediate structures? J. Mol. Biol.\u00a0385, 665\u2013674 (2009)","journal-title":"J. Mol. Biol."},{"issue":"38","key":"21_CR22","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1002\/chin.199838349","volume":"29","author":"W.P. Walters","year":"1998","unstructured":"Walters, W.P., Stahl, M.T., Murco, M.A.: Cheminform abstract: Virtual screening-an overview. ChemInform\u00a029(38), 160\u2013178 (1998)","journal-title":"ChemInform"},{"key":"21_CR23","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1038\/nrd1129","volume":"2","author":"S.J. Teague","year":"2003","unstructured":"Teague, S.J.: Implications of protein flexibility for drug discovery. Nat. Rev. Drug. Discov.\u00a02, 527\u2013541 (2003)","journal-title":"Nat. Rev. Drug. Discov."},{"key":"21_CR24","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1016\/j.jmb.2004.02.015","volume":"337","author":"B.Q. Wei","year":"2004","unstructured":"Wei, B.Q., Weaver, L.H., Ferrari, A.M., Matthews, B.W., Shoichet, B.K.: Testing a flexible-receptor docking algorithm in a model binding site. J. Mol. Biol.\u00a0337, 1161\u20131182 (2004)","journal-title":"J. Mol. Biol."},{"key":"21_CR25","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/S1093-3263(00)00036-X","volume":"18","author":"H.B. Broughton","year":"2000","unstructured":"Broughton, H.B.: A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. J. Mol. Graph. Model.\u00a018, 247\u2013257 (2000)","journal-title":"J. Mol. Graph. Model."},{"issue":"1","key":"21_CR26","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/0022-2836(91)90883-8","volume":"218","author":"L. Holm","year":"1991","unstructured":"Holm, L., Sander, C.: 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. Journal of Molecular Biology\u00a0218(1), 183\u2013194 (1991)","journal-title":"Journal of Molecular Biology"},{"issue":"15","key":"21_CR27","doi-asserted-by":"publisher","first-page":"2714","DOI":"10.1002\/elps.1150181505","volume":"18","author":"N. Guex","year":"1997","unstructured":"Guex, N., Peitsch, M.C.: Swiss-model and the swiss-pdbviewer: an environment for comparative protein modeling. Electrophoresis\u00a018(15), 2714\u20132723 (1997)","journal-title":"Electrophoresis"},{"issue":"3","key":"21_CR28","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1006\/jmbi.1996.0897","volume":"267","author":"G. Jones","year":"1997","unstructured":"Jones, G., Willett, P., Glen, R.C., Leach, A.R., Taylor, R.: Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology\u00a0267(3), 727\u2013748 (1997)","journal-title":"Journal of Molecular Biology"}],"container-title":["Lecture Notes in Computer Science","Algorithms in Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-33122-0_21.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,28]],"date-time":"2024-04-28T19:26:23Z","timestamp":1714332383000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-33122-0_21"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783642331213","9783642331220"],"references-count":28,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-33122-0_21","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2012]]}}}