{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T03:46:19Z","timestamp":1759117579051},"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2014,7,24]],"date-time":"2014-07-24T00:00:00Z","timestamp":1406160000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003719","type":"journal-article","created":{"date-parts":[[2014,7,24]],"date-time":"2014-07-24T18:33:24Z","timestamp":1406226804000},"page":"e1003719","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial"],"prefix":"10.1371","volume":"10","author":[{"given":"Benjamin T.","family":"Miller","sequence":"first","affiliation":[]},{"given":"Rishi P.","family":"Singh","sequence":"additional","affiliation":[]},{"given":"Vinushka","family":"Schalk","sequence":"additional","affiliation":[]},{"given":"Yuri","family":"Pevzner","sequence":"additional","affiliation":[]},{"given":"Jingjun","family":"Sun","sequence":"additional","affiliation":[]},{"given":"Carrie S.","family":"Miller","sequence":"additional","affiliation":[]},{"given":"Stefan","family":"Boresch","sequence":"additional","affiliation":[]},{"given":"Toshiko","family":"Ichiye","sequence":"additional","affiliation":[]},{"given":"Bernard R.","family":"Brooks","sequence":"additional","affiliation":[]},{"given":"H. Lee","family":"Woodcock","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,7,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1021\/ed085p1071","article-title":"Using Molecular Dynamics Simulation To Reinforce Student Understanding of Intermolecular Forces","volume":"85","author":"PR Burkholder","year":"2008","journal-title":"J Chem Ed"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1021\/ed075p241","article-title":"Integration of Computational Chemistry into the Chemistry Curriculum","volume":"75","author":"NH Martin","year":"1998","journal-title":"J Chem Ed"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: The Biomolecular Simulation Program","volume":"30","author":"BR Brooks","year":"2009","journal-title":"J Comput Chem"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1021\/ci800133b","article-title":"CHARMMing: A new, flexible web portal for CHARMM","volume":"48","author":"BT Miller","year":"2008","journal-title":"J Chem Inf Model"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A web-based graphical user interface for CHARMM","volume":"29","author":"S Jo","year":"2008","journal-title":"J Comput Chem"},{"key":"ref6","unstructured":"Woods research group, Complex Carboyhdrate Research Center, University of Georgia (2005\u20132014). Glycam Biomolecule Builder. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.glycam.com\" xlink:type=\"simple\">http:\/\/www.glycam.com<\/ext-link> Accessed 25 June 2014."},{"key":"ref7","doi-asserted-by":"crossref","first-page":"W240","DOI":"10.1093\/nar\/gkp358","article-title":"Web 3DNA - A web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures","volume":"37","author":"G Zheng","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"W610","DOI":"10.1093\/nar\/gkh368","article-title":"ElN\u00e9mo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement","volume":"32","author":"K Suhre","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref9","unstructured":"Zheng W (2007\u20132014). AD-ENM Web Server. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/enm.lobos.nih.gov\" xlink:type=\"simple\">http:\/\/enm.lobos.nih.gov<\/ext-link> Accessed 25 June 2014."},{"key":"ref10","unstructured":"Schmidt J, Polik W (2014). WebMO, version 14.0. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.webmo.net\" xlink:type=\"simple\">http:\/\/www.webmo.net<\/ext-link> Accessed 25 June 2014."},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1021\/ed085p1288","article-title":"Quantum Chemistry Laboratory at Home","volume":"85","author":"JC Paniagua","year":"2008","journal-title":"J Chem Ed"},{"key":"ref12","unstructured":"Frenkel D, Smit B (2007) Understanding Molecular Simulation, Second Edition: From Algorithms to Applications. San Diego: Academic Press."},{"key":"ref13","unstructured":"Leach A (2001) Molecular Modelling: Principles and Applications. 2nd Edition. Harlow: Prentice Hall."},{"key":"ref14","doi-asserted-by":"crossref","unstructured":"Allen MP, Tildesley DJ (1989) Computer Simulation of Liquids. Oxford: Oxford University Press.","DOI":"10.1063\/1.2810937"},{"key":"ref15","unstructured":"Dill K, Bromberg S (2002) Molecular Driving Forces: Statistical Thermodynamics in Chemistry &amp; Biology. New York: Garland Science."},{"key":"ref16","doi-asserted-by":"crossref","unstructured":"Kessel A, Ben-Tal N (2010) Introduction to Proteins: Structure, Function, and Motion. CRC Press.","DOI":"10.1201\/b10456"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1002\/prot.22263","article-title":"Binding and release of cholesterol in the OSH4 protein of yeast","volume":"75","author":"RP Singh","year":"2009","journal-title":"Proteins"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1038\/nature03923","article-title":"Structural mechanism for sterol sensing and transport by OSBP-related proteins","volume":"437","author":"YJ Im","year":"2005","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"7830","DOI":"10.1021\/jp101759q","article-title":"Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types","volume":"114","author":"JB Klauda","year":"2010","journal-title":"J Phys Chem B"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N\u22c5log(N) method for Ewald sums in large systems","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"7070","DOI":"10.1063\/1.476320","article-title":"Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential","volume":"108","author":"S Bogusz","year":"1998","journal-title":"J Chem Phys"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1146\/annurev.biophys.37.092707.153558","article-title":"The Protein Folding Problem","volume":"37","author":"KA Dill","year":"2008","journal-title":"Ann Rev Biophys"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"17845","DOI":"10.1073\/pnas.1201811109","article-title":"Protein folding kinetics and thermodynamics from atomistic simulation","volume":"109","author":"S Piana","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"12935","DOI":"10.1021\/jp4020993","article-title":"Atomistic description of the folding of a dimeric protein","volume":"117","author":"S Piana","year":"2013","journal-title":"J Phys Chem B"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"5915","DOI":"10.1073\/pnas.1218321110","article-title":"Atomic-level description of ubiquitin folding","volume":"110","author":"S Piana","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nature03680","article-title":"Structure of the cross-<italic>\u03b2<\/italic> spine of amyloid-like fibrils","volume":"435","author":"R Nelson","year":"2005","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/j.cplett.2003.10.013","article-title":"Self-guided Langevin dynamics simulation method","volume":"381","author":"X Wu","year":"2003","journal-title":"Chem Phys Lett"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/0022-2836(76)90311-9","article-title":"Theoretical Studies of Enzymic Reactions - Dielectric, Electrostatic and Steric Stabilization of Carbonium-Ion in Reaction of Lysozyme","volume":"103","author":"A Warshel","year":"1976","journal-title":"J Mol Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1002\/jcc.540070604","article-title":"A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the <inline-formula><inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"info:doi\/10.1371\/journal.pcbi.1003719.e001\" xlink:type=\"simple\"><\/inline-graphic><\/inline-formula> exchange reaction and gas phase protonation of polyethers","volume":"7","author":"UC Singh","year":"1986","journal-title":"J Comput Chem"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1002\/jcc.540110605","article-title":"A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations","volume":"11","author":"MJ Field","year":"1990","journal-title":"J Comput Chem"},{"key":"ref32","unstructured":"The Nobel Prize in Chemistry 2013. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.nobelprize.org\/nobel_prizes\/chemistry\/laureates\/2013\/\" xlink:type=\"simple\">http:\/\/www.nobelprize.org\/nobel_prizes\/chemistry\/laureates\/2013\/<\/ext-link> Accessed 25 June 2014."},{"key":"ref33","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1126\/science.1088172","article-title":"How enzymes work: analysis by modern rate theory and computer simulations","volume":"303","author":"M Garcia-Viloca","year":"2004","journal-title":"Science"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/j.sbi.2008.07.003","article-title":"Multiscale methods for macromolecular simulations","volume":"18","author":"P Sherwood","year":"2008","journal-title":"Curr Opin Struct Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1002\/anie.200802019","article-title":"QM\/MM methods for biomolecular systems","volume":"48","author":"HM Senn","year":"2009","journal-title":"Angew Chem Int Ed Engl"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1021\/ar900171c","article-title":"Advances in Quantum and Molecular Mechanical (QM\/MM) Simulations for Organic and Enzymatic Reactions","volume":"43","author":"O Acevedo","year":"2010","journal-title":"Acc Chem Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields","volume":"31","author":"K Vanommeslaeghe","year":"2010","journal-title":"J Comput Chem"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3144","DOI":"10.1021\/ci300363c","article-title":"Automation of the CHARMM General Force Field (CGenFF) I: Bond and perception and atom typing","volume":"52","author":"K Vanommeslaeghe","year":"2012","journal-title":"J Chem Inf Mod"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"3155","DOI":"10.1021\/ci3003649","article-title":"Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges","volume":"52","author":"K Vanommeslaeghe","year":"2012","journal-title":"J Chem Inf Model"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"3172","DOI":"10.1039\/B517914A","article-title":"Advances in methods and algorithms in a modern quantum chemistry program package","volume":"8","author":"Y Shao","year":"2006","journal-title":"Phys Chem Chem Phys"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1485","DOI":"10.1002\/jcc.20587","article-title":"Interfacing Q-Chem and CHARMM to perform QM\/MM reaction path calculations","volume":"28","author":"HL Woodcock","year":"2007","journal-title":"J Comput Chem"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1073\/pnas.97.6.2544","article-title":"Mechanisms and kinetics of <italic>\u03b2<\/italic>-hairpin formation","volume":"97","author":"DK Klimov","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1021\/jp036508g","article-title":"Coarse grained model for semiquantitative lipid simulations","volume":"108","author":"SJ Marrink","year":"2004","journal-title":"J Phys Chem B"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2697","DOI":"10.1021\/ja0569104","article-title":"Insertion and Assembly of Membrane Proteins via Simulation","volume":"128","author":"PJ Bond","year":"2006","journal-title":"J Am Chem Soc"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"10037","DOI":"10.1073\/pnas.181342398","article-title":"Electrostatics of nanosystems: Application to microtubules and the ribosome","volume":"98","author":"NA Baker","year":"2001","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"2798","DOI":"10.1002\/prot.22794","article-title":"Fold versus sequence effects on the driving force for protein-mediated electron transfer","volume":"78","author":"BS Perrin","year":"2010","journal-title":"Proteins: Struct, Funct, Bioinf"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1002\/jcc.540150702","article-title":"New spherical-cutoff methods for long-range forces in macromolecular simulation","volume":"15","author":"PJ Steinbach","year":"1994","journal-title":"J Comput Chem"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1006\/jmbi.1993.1143","article-title":"Atomic Resolution (0.83 \u00c5) Crystal Structure of the Hydrophobic Protein Crambin at 130 K","volume":"230","author":"MM Teeter","year":"1993","journal-title":"J Mol Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1002\/ijch.201300024","article-title":"JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia","volume":"53","author":"RM Hanson","year":"2013","journal-title":"Isr J Chem"},{"key":"ref50","unstructured":"Nakane T (2012). GLmol - Molecular Viewer on WebGL\/Javascript, Version 0.47. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/webglmol.sourceforge.jp\/index-en.html\" xlink:type=\"simple\">http:\/\/webglmol.sourceforge.jp\/index-en.html<\/ext-link> Accessed 25 June 2014.."},{"key":"ref51","doi-asserted-by":"crossref","unstructured":"Willighagen E, Howard M (2007). Fast and Scriptable Molecular Graphics in Web Browsers without Java3D: Nature Precedings. doi:10.1038\/npre.2007.50.1. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/precedings.nature.com\/documents\/50\/version\/1\" xlink:type=\"simple\">http:\/\/precedings.nature.com\/documents\/50\/version\/1<\/ext-link> Accessed 25 June 2014..","DOI":"10.1038\/npre.2007.50.1"},{"key":"ref52","unstructured":"Department of Homeland Security: USCERT (2013). Alert (TA13-010A): Oracle Java 7 Security Manager Bypass Vulnerability. Available <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.us-cert.gov\/ncas\/alerts\/ta13-010a\" xlink:type=\"simple\">http:\/\/www.us-cert.gov\/ncas\/alerts\/ta13-010a<\/ext-link> Accessed 25 June 2014."},{"key":"ref53","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD \u2013 Visual Molecular Dynamics","volume":"14","author":"W Humphrey","year":"1996","journal-title":"J Mol Graph"},{"key":"ref54","unstructured":"Schr\u00f6dinger LLC (2010). The PyMOL Molecular Graphics System, Version 1.3r1. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.pymol.org\/\" xlink:type=\"simple\">http:\/\/www.pymol.org\/<\/ext-link> Accessed 25 June 2014."},{"key":"ref55","unstructured":"Nussinov R (2013). The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/blogs.plos.org\/biologue\/2013\/10\/18\/the-significance-of-the-2013-nobel-prize-in-chemistry-and-the-challenges-ahead\/\" xlink:type=\"simple\">http:\/\/blogs.plos.org\/biologue\/2013\/10\/18\/the-significance-of-the-2013-nobel-prize-in-chemistry-and-the-challenges-ahead\/<\/ext-link> Accessed 25 June 2014."},{"key":"ref56","unstructured":"Ichiye T (2014). CHEM-573 Computational Methods for Biological Macromolecules. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/courses.georgetown.edu\/index.cfm?CourseID=CHEM-573\" xlink:type=\"simple\">http:\/\/courses.georgetown.edu\/index.cfm?CourseID=CHEM-573<\/ext-link> Accessed 25 June 2014."},{"key":"ref57","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1016\/0022-2836(87)90679-6","article-title":"Structure of ubiquitin refined at 1.8 \u00c5 resolution","volume":"194","author":"S Vijay-Kumar","year":"1987","journal-title":"J Mol Biol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003719","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T06:41:02Z","timestamp":1717137662000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003719"}},"subtitle":[],"editor":[{"given":"Qiang","family":"Cui","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,7,24]]},"references-count":57,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2014,7,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003719","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,7,24]]}}}