{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,27]],"date-time":"2024-01-27T05:38:04Z","timestamp":1706333884628},"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2005,6,24]],"date-time":"2005-06-24T00:00:00Z","timestamp":1119571200000},"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.0010008","type":"journal-article","created":{"date-parts":[[2005,6,24]],"date-time":"2005-06-24T21:29:49Z","timestamp":1119648589000},"page":"e8","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a \u03b2-Hairpin"],"prefix":"10.1371","volume":"1","author":[{"given":"Laxmi","family":"Parida","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruhong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2005,6,24]]},"reference":[{"key":"pcbi-0010008-b01","doi-asserted-by":"crossref","unstructured":"FengJParidaLZhouR 2005 Protein folding trajectory analysis using patterned clusters [abstract]. Asia Pacific Bioinformatics Conference; 2005 17\u201321 Jan; Singapore","DOI":"10.1142\/9781860947322_0010"},{"key":"pcbi-0010008-b02","unstructured":"FershtAR 1999 Structure and mechanism in protein science New York W.H. Freeman 631 p."},{"key":"pcbi-0010008-b03","doi-asserted-by":"crossref","unstructured":"BrooksCLOnuchicJNWalesDJ 2001 Taking a walk on a landscape. Science 293 612","DOI":"10.1126\/science.1062559"},{"key":"pcbi-0010008-b04","doi-asserted-by":"crossref","unstructured":"DobsonCMSaliAKarplusM 1998 Protein folding: A perspective from theory and experiment. Angew Chem Int Ed Engl 37 868","DOI":"10.1002\/(SICI)1521-3773(19980420)37:7<868::AID-ANIE868>3.0.CO;2-H"},{"key":"pcbi-0010008-b05","doi-asserted-by":"crossref","unstructured":"BrooksCLGruebeleMOnuchicJNWolynesPG 1998 Chemical physics of protein folding. Proc Natl Acad Sci U S A 95 11037","DOI":"10.1073\/pnas.95.19.11037"},{"key":"pcbi-0010008-b06","doi-asserted-by":"crossref","unstructured":"SavenJG 2003 Connecting statistical and optimized potentials for protein folding via a generalized foldability criterion. J Chem Phys 118 6133 6136","DOI":"10.1063\/1.1565995"},{"key":"pcbi-0010008-b07","doi-asserted-by":"crossref","unstructured":"ZhouRHuangXMarguliusCJBerneBJ 2004 Hydrophobic collapse in multidomain protein folding. Science 305 1605","DOI":"10.1126\/science.1101176"},{"key":"pcbi-0010008-b08","doi-asserted-by":"crossref","unstructured":"SimonsKTBonneauRRuczinskiIBakerD 1999 Structure prediction of casp iii targets using rosetta. Proteins 37 171","DOI":"10.1002\/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z"},{"key":"pcbi-0010008-b09","doi-asserted-by":"crossref","unstructured":"XuDCrawfordOLocascioPXuY 2001 Application of prospect in casp4: Characterizing protein structures with new folds. Proteins S5: 140\u2013148.","DOI":"10.1002\/prot.10022"},{"key":"pcbi-0010008-b10","doi-asserted-by":"crossref","unstructured":"ZhouRSilvermanBDRoyyuruAAthmaP 2003 Spatial profiling of protein hydrophobicity: Native vs. decoy structures. Proteins52: 561.","DOI":"10.1002\/prot.10419"},{"key":"pcbi-0010008-b11","doi-asserted-by":"crossref","unstructured":"BlancoFJRivasGSerranoL 1994 A short linear peptide that folds in a native stable \u03b2-hairpin in aqueous solution. Nat Struct Biol 1 584","DOI":"10.1038\/nsb0994-584"},{"key":"pcbi-0010008-b12","doi-asserted-by":"crossref","unstructured":"BlancoFJSerranoL 1994 Folding of protein g b1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur J Biochem 230 634","DOI":"10.1111\/j.1432-1033.1995.tb20605.x"},{"key":"pcbi-0010008-b13","doi-asserted-by":"crossref","unstructured":"MunozVThompsonPAHofrichterJEatonWA 1997 Folding dynamics and mechanism of \u03b2-hairpin formation. Nature 390 196","DOI":"10.1038\/36626"},{"key":"pcbi-0010008-b14","doi-asserted-by":"crossref","unstructured":"MunozVHenryERHofrichterJEatonWA 1998 A statistical mechanical model for \u03b2-hairpin kinetics. Proc Natl Acad Sci U S A 95 5872","DOI":"10.1073\/pnas.95.11.5872"},{"key":"pcbi-0010008-b15","doi-asserted-by":"crossref","unstructured":"DuDZhuYHuangCYGaiF 2004 Understanding the key factors that control the rate of \u03b2-hairpin folding. Proc Natl Acad Sci U S A 101 15915","DOI":"10.1073\/pnas.0405904101"},{"key":"pcbi-0010008-b16","doi-asserted-by":"crossref","unstructured":"SnowCDQiuLDuDGaiFHagenSJ 2004 Trp Zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proc Natl Acad Sci U S A 101 4077","DOI":"10.1073\/pnas.0305260101"},{"key":"pcbi-0010008-b17","doi-asserted-by":"crossref","unstructured":"DyerRBManessSJPetersonESFranzenSFeisinmeyerRM 2004 The mechanism of \u03b2-hairpin formation. Biochemistry 43 11560","DOI":"10.1021\/bi049177m"},{"key":"pcbi-0010008-b18","doi-asserted-by":"crossref","unstructured":"ZagrovicBSorinEJPandeVS 2001 \u03b2-hairpin folding simulation in atomistic detail. J Mol Biol 313 151","DOI":"10.1006\/jmbi.2001.5033"},{"key":"pcbi-0010008-b19","doi-asserted-by":"crossref","unstructured":"YodaTSugitaYOkamotoY 2004 Comparisons of force fields for proteins by generalized-ensemble simulations. Chem Phys Lett 386 460","DOI":"10.1016\/j.cplett.2004.01.078"},{"key":"pcbi-0010008-b20","doi-asserted-by":"crossref","unstructured":"GarciaAESanbonmatsuKY 2001 Exploring the energy landscape of a \u03b2- hairpin in explicit solvent. Proteins 42 345","DOI":"10.1002\/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO;2-H"},{"key":"pcbi-0010008-b21","doi-asserted-by":"crossref","unstructured":"ZhouRBerneBJGermainR 2001 The free energy landscape for \u03b2-hairpin folding in explicit water. Proc Natl Acad Sci 98 14931","DOI":"10.1073\/pnas.201543998"},{"key":"pcbi-0010008-b22","doi-asserted-by":"crossref","unstructured":"GarciaAE 2001 Large-amplitude nonlinear motions in proteins. Phys Rev Lett 42 2696","DOI":"10.1103\/PhysRevLett.68.2696"},{"key":"pcbi-0010008-b23","doi-asserted-by":"crossref","unstructured":"ZhouR 2001 Free energy landscape of protein folding in water: Explicit vs. implicit solvent. Proteins 98 148","DOI":"10.1002\/prot.10483"},{"key":"pcbi-0010008-b24","doi-asserted-by":"crossref","unstructured":"SugitaYOkamotoY 1999 Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314 141","DOI":"10.1016\/S0009-2614(99)01123-9"},{"key":"pcbi-0010008-b25","doi-asserted-by":"crossref","unstructured":"ZhouR 2003 Trp-cage: Folding free energy landscape in explicit water. Proc Natl Acad Sci U S A 100 13280","DOI":"10.1073\/pnas.2233312100"},{"key":"pcbi-0010008-b26","doi-asserted-by":"crossref","unstructured":"PandeVSRokhsarDS 1999 Molecular dynamics simulations of unfolding and refolding of a \u03b2-hairpin fragment of protein g. Proc Natl Acad Sci U S A 96 9062","DOI":"10.1073\/pnas.96.16.9062"},{"key":"pcbi-0010008-b27","doi-asserted-by":"crossref","unstructured":"DinnerARLazaridisTKarplusM 1999 Understanding \u03b2-hairpin formation. Proc Natl Acad Sci U S A 96 9068","DOI":"10.1073\/pnas.96.16.9068"},{"key":"pcbi-0010008-b28","doi-asserted-by":"crossref","unstructured":"RoccatanoDAmadeiADi NolaABerendsenHJ 1999 A molecular dynamics study of the 41\u201356 \u03b2-hairpin from b1 domain of protein g. Protein Sci 10 2130","DOI":"10.1110\/ps.8.10.2130"},{"key":"pcbi-0010008-b29","doi-asserted-by":"crossref","unstructured":"KolinskiAIlkowskiBSkolnickJ 1999 Dynamics and thermodynamics of \u03b2-hairpin assembly: Insights from various simulation techniques. Biophys J 77 2942","DOI":"10.1016\/S0006-3495(99)77127-4"},{"key":"pcbi-0010008-b30","doi-asserted-by":"crossref","unstructured":"MaBNussinovR 2000 Molecular dynamics simulations of a \u03b2-hairpin fragment of protein g: Balance between side-chain and backbone forces. J Mol Bio 296 1091","DOI":"10.1006\/jmbi.2000.3518"},{"key":"pcbi-0010008-b31","doi-asserted-by":"crossref","unstructured":"KlimovDKThirumalaiD 2000 Mechanism and kinetics of \u03b2-hairpin formation. Proc Natl Acad Sci U S A 97 2544","DOI":"10.1073\/pnas.97.6.2544"},{"key":"pcbi-0010008-b32","doi-asserted-by":"crossref","unstructured":"ZhouRBerneBJ 2002 Can a continuum solvent model reproduce the free energy landscape of a \u03b2-hairpin folding in water? Proc Natl Acad Sci 99 12777","DOI":"10.1073\/pnas.142430099"},{"key":"pcbi-0010008-b33","doi-asserted-by":"crossref","unstructured":"JorgensenWLMaxwellDTirado-RivesJ 1996 Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118 11225","DOI":"10.1021\/ja9621760"},{"key":"pcbi-0010008-b34","doi-asserted-by":"crossref","unstructured":"BerendsenHJCPostmaJPMvan GunsterenWFHermansJ 1981 Interaction models for water in relation to protein hydration. In: PullmanB Intermolecular forces Dordrecht (Netherlands) Reidel pp 331 342","DOI":"10.1007\/978-94-015-7658-1_21"},{"key":"pcbi-0010008-b35","doi-asserted-by":"crossref","unstructured":"Klein-SeetharamanJOikawaMGrimshawSBWirmerJDuchardtE 2002 Long-range interactions within a nonnative protein. Science 295 1719","DOI":"10.1126\/science.1067680"},{"key":"pcbi-0010008-b36","doi-asserted-by":"crossref","unstructured":"LepreJRiceJTuYStolovitzkyG 2004 Genes@Work: An efficient algorithm for pattern discovery and multi-variate feature selection in gene expression data. Bioinformatics 7 1033 1044","DOI":"10.1093\/bioinformatics\/bth035"},{"key":"pcbi-0010008-b37","doi-asserted-by":"crossref","unstructured":"ParidaL 2000 Some results on flexible-pattern discovery. Combinatorial Pattern Matching (CPM2000) LNCS 1848 33","DOI":"10.1007\/3-540-45123-4_5"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0010008","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,27]],"date-time":"2024-01-27T04:47:34Z","timestamp":1706330854000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0010008"}},"subtitle":[],"editor":[{"given":"Luhua","family":"Lai","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2005,6,24]]},"references-count":37,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,6,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0010008","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,6,24]]}}}