{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T09:56:05Z","timestamp":1790589365469,"version":"4.1.0"},"reference-count":69,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2015,8,24]],"date-time":"2015-08-24T00:00:00Z","timestamp":1440374400000},"content-version":"vor","delay-in-days":365,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1K22HL088341-01A1"],"award-info":[{"award-number":["1K22HL088341-01A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000165","name":"Division of Chemistry","doi-asserted-by":"publisher","award":["CHE1156853"],"award-info":[{"award-number":["CHE1156853"]}],"id":[{"id":"10.13039\/100000165","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006151","name":"Basic Energy Sciences","doi-asserted-by":"publisher","award":["DE-SC0011297TDD"],"award-info":[{"award-number":["DE-SC0011297TDD"]}],"id":[{"id":"10.13039\/100006151","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing\u2019s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of \u201cre-dockings\u201d with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing\u2019s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.<\/jats:p>","DOI":"10.1021\/ci500322k","type":"journal-article","created":{"date-parts":[[2014,8,24]],"date-time":"2014-08-24T10:36:26Z","timestamp":1408876586000},"page":"2612-2620","source":"Crossref","is-referenced-by-count":21,"title":["Fragment-Based\nDocking: Development of the CHARMMing\nWeb User Interface as a Platform\nfor Computer-Aided Drug Design"],"prefix":"10.1021","volume":"54","author":[{"given":"Yuri","family":"Pevzner","sequence":"first","affiliation":[{"name":"University of South Florida , , 4202 E. Fowler Ave., CHE205 , , ,","place":["Tampa, Florida, United States, 33620-5250"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilie","family":"Frugier","sequence":"additional","affiliation":[{"name":"University of Zurich , , ,","place":["Zurich, Switzerland, CH-8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinushka","family":"Schalk","sequence":"additional","affiliation":[{"name":"University of South Florida , , 4202 E. Fowler Ave., CHE205 , , ,","place":["Tampa, Florida, United States, 33620-5250"]},{"name":"New College of Florida , , , ,","place":["Sarasota, Florida, United States, 34243"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amedeo","family":"Caflisch","sequence":"additional","affiliation":[{"name":"University of Zurich , , ,","place":["Zurich, Switzerland, CH-8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. Lee","family":"Woodcock","sequence":"additional","affiliation":[{"name":"University of South Florida , , 4202 E. Fowler Ave., CHE205 , , ,","place":["Tampa, Florida, United States, 33620-5250"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2014,8,24]]},"reference":[{"key":"2026092805063665900_cit1","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1517\/17460441.2013.794780","article-title":"Automated\ndocking for novel drug discovery","volume":"8","author":"Bello","year":"2013","journal-title":"Expert Opin.\nDrug Discovery"},{"key":"2026092805063665900_cit2","first-page":"1","article-title":"Towards a sustainable system of drug\ndevelopment","author":"Moors","year":"2014","journal-title":"Drug Discovery Today"},{"key":"2026092805063665900_cit3","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/S1359-6446(04)03363-X","article-title":"The case\nfor open-source software in drug discovery","volume":"10","author":"DeLano","year":"2005","journal-title":"Drug Discovery Today"},{"key":"2026092805063665900_cit4","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/S1359-6446(05)03692-5","article-title":"Optimizing the use of open-source software applications\nin drug discovery","volume":"11","author":"Geldenhuys","year":"2006","journal-title":"Drug Discovery Today"},{"key":"2026092805063665900_cit5","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1002\/prot.340080302","article-title":"Automated docking\nof substrates to proteins by simulated\nannealing","volume":"8","author":"Goodsell","year":"1990","journal-title":"Proteins"},{"key":"2026092805063665900_cit6","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s10822-010-9395-8","article-title":"Computer-aided drug design platform\nusing PyMOL","volume":"25","author":"Lill","year":"2011","journal-title":"J. Comput.-Aided. Mol. Des."},{"key":"2026092805063665900_cit7","volume-title":"Maestro","year":"2013"},{"key":"2026092805063665900_elcit681094281","unstructured":"Discovery Studio Modeling\nEnvironment; Accelrys\nSoftware, Inc.: San Diego, CA, 2013."},{"key":"2026092805063665900_elcit1748876332","unstructured":"Molecular Operating Environment\n(MOE), 2013.08; Chemical Computing Group,\nInc.: Montreal,\nQuebec, Canada, 2013."},{"key":"2026092805063665900_cit10","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.jmgm.2013.06.002","article-title":"The emerging role\nof cloud computing in molecular modelling","volume":"44","author":"Ebejer","year":"2013","journal-title":"J.\nMol. Graph. Model."},{"key":"2026092805063665900_cit11","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1002\/(SICI)1096-987X(199604)17:5\/6<490::AID-JCC1>3.0.CO;2-P","article-title":"Merck molecular\nforce field. I. 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