CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
文献类型：期刊论文
| 作者 | Hwang, Wonmuk59,60,61,62; Austin, Steven L.58; Blondel, Arnaud57; Boittier, Eric D.56; Boresch, Stefan55; Buck, Matthias54; Buckner, Joshua53; Caflisch, Amedeo52; Chang, Hao-Ting51; Cheng, Xi50 |
| 刊名 | JOURNAL OF PHYSICAL CHEMISTRY B
 |
| 出版日期 | 2024-09-20 |
| 页码 | 67 |
| ISSN号 | 1520-6106 |
| DOI | 10.1021/acs.jpcb.4c04100 |
| 通讯作者 | Hwang, Wonmuk(hwm@tamu.edu) ; Brooks, Charles L.(brookscl@umich.edu) ; Brooks III, Bernard R.() |
| 英文摘要 | Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program. |
| WOS关键词 | MOLECULAR-DYNAMICS SIMULATIONS ; POLARIZABLE FORCE-FIELD ; BINDING FREE-ENERGY ; GENERALIZED BORN MODEL ; PARTICLE MESH EWALD ; GUI-MEMBRANE-BUILDER ; INTERMOLECULAR POTENTIAL FUNCTION ; REPLICA-EXCHANGE SIMULATIONS ; PROTEIN-STRUCTURE PREDICTION ; NONEQUILIBRIUM WORK METHODS |
| 资助项目 | U.S. National Institutes of Health (NIH) ; U.S. National Science Foundation (NSF) ; Intramural Research Program of the NIH, National Heart, Lung, and Blood Institute[ZIA HL001051] ; Intramural Research Program of the NIH, National Heart, Lung, and Blood Institute[ZIA HL001052] ; Intramural Research Program of the NIH, National Heart, Lung, and Blood Institute[ZIA HL000340] ; NIH[R35GM137058] ; NIH[R35GM141930] ; NIH[R35GM126948] ; NIH[R01GM046736] ; NIH[R01GM138472] ; NIH[R35GM133754] ; NIH[R35GM131710] ; NIH[R01GM132481] ; NIH[R21GM148895] ; NIH[R01GM039478] ; NIH[R01GM135392] ; NIH[R35GM148261] ; NIH[R01GM129519] ; NIH[R01GM143810] ; NIH[R01GM140316] ; Swiss National Science Foundation[310030-212195] ; Swiss National Science Foundation[215088] ; Swiss National Science Foundation[219779] ; National Science and Technology Council of Taiwan[112-2113-M-A49-018-MY3] ; European Research Council Consolidator Grant[NANOVR 866559] ; Intramural program of the National Library of Medicine at the NIH ; NSF[MCB-211172] ; NSF[MCB-1855942] ; NSF[MCB-1919096] ; Office of Science, U.S. Department of Energy[DE-AC02-06CH11357] ; NCCR MUST ; University of Basel |
| WOS研究方向 | Chemistry |
| 语种 | 英语 |
| WOS记录号 | WOS:001321304100001 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/313651]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Hwang, Wonmuk; Brooks, Charles L.; Brooks III, Bernard R. |
| 作者单位 | 1.Univ Strasbourg, ISIS, Lab Chim Biophys, F-67000 Strasbourg, France 2.NIH, Eunice Kennedy Shriver Natl Inst Child Hlth & Huma, Bethesda, MD 20892 USA 3.Carleton Univ, Dept Chem, Ottawa, ON K1S 5B6, Canada 4.Univ Chicago, Dept Chem, Chicago, IL 60637 USA 5.Indian Inst Technol Hyderabad, Dept Biotechnol, Kandi 502284, Telangana State, India 6.Fudan Univ, Sch Pharm, Shanghai 201203, Peoples R China 7.Indiana Univ Indianapolis, Dept Chem & Chem Biol, Indianapolis, IN 46202 USA 8.Purdue Univ, Borch Dept Med Chem & Mol Pharmacol, W Lafayette, IN 47907 USA 9.Univ Bologna, Dipartimento Fis & Astron, I-40127 Bologna, Italy 10.Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA |
| 推荐引用方式 GB/T 7714 | Hwang, Wonmuk,Austin, Steven L.,Blondel, Arnaud,et al. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2024:67. |
| APA | Hwang, Wonmuk.,Austin, Steven L..,Blondel, Arnaud.,Boittier, Eric D..,Boresch, Stefan.,...&Karplus, Martin.(2024).CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.JOURNAL OF PHYSICAL CHEMISTRY B,67. |
| MLA | Hwang, Wonmuk,et al."CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed".JOURNAL OF PHYSICAL CHEMISTRY B (2024):67. |
入库方式： OAI收割
来源：上海药物研究所
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