CHARMM-GUI 10 years for biomolecular modeling and simulation

doi:10.1002/jcc.24660

CORC > 上海药物研究所 > 中国科学院上海药物研究所 > 药物发现与设计中心

	CHARMM-GUI 10 years for biomolecular modeling and simulation
	Jo, Sunhwan 1; Cheng, Xi 2; Lee, Jumin 3,4; Kim, Seonghoon 3,4; Park, Sang-Jun 3,4; Patel, Dhilon S.3,4; Beaven, Andrew H.5; Lee, Kyu Il 3,4; Rui, Huan 6; Park, Soohyung 3,4
刊名	JOURNAL OF COMPUTATIONAL CHEMISTRY
	2017-06-05
卷号	38 期号:15 页码:1114-1124
关键词	Coarse-grained simulation Glycan Membranes mmCIF Protein-ligand interactions
ISSN号	0192-8651
DOI	10.1002/jcc.24660
文献子类	Review
英文摘要	CHARMM-GUI, , is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. (c) 2016 Wiley Periodicals, Inc.
资助项目	NSF[MCB-0918374] ; NSF[MCB-1157677] ; NSF[MCB-1516154] ; NSF[DBI-1145987] ; NSF[DBI-1707207] ; NSF[IIA-1359530] ; NSF[MCB-1149187] ; NSF[DBI-1145652] ; NIH[GM092950] ; NIH[GM087519] ; NIH[GM072558] ; NIH[GM070855] ; NIH[GM051501] ; Extreme Science and Engineering Discovery Environment (XSEDE) allocations[MCB-070009] ; Extreme Science and Engineering Discovery Environment (XSEDE) allocations[MCB-100139] ; Extreme Science and Engineering Discovery Environment (XSEDE) allocations[NSF ACI-1053575]
WOS关键词	MOLECULAR-DYNAMICS SIMULATIONS ; FREE-ENERGY CALCULATIONS ; GENERAL FORCE-FIELD ; BINDING FREE-ENERGY ; HAMILTONIAN REPLICA-EXCHANGE ; CLASSICAL DRUDE OSCILLATOR ; COARSE-GRAINED SIMULATIONS ; MEMBRANE-MIMETIC MODEL ; PHOSPHOLIPID-MEMBRANES ; COMPUTER-SIMULATIONS
WOS研究方向	Chemistry
语种	英语
出版者	WILEY
WOS记录号	WOS:000399970200002
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/272621]
专题	药物发现与设计中心中科院受体结构与功能重点实验室新药研究国家重点实验室
通讯作者	Im, Wonpil
作者单位	1.Argonne Natl Lab, Leadership Comp Facil, 9700 Cass Ave, Argonne, IL USA; 2.Chinese Acad Sci, Drug Discovery & Design Ctr, State Key Lab Drug Res, Shanghai Inst Mat Med, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China; 3.Lehigh Univ, Dept Biol Sci, Bethlehem, PA 18015 USA; 4.Lehigh Univ, Bioengn Program, Bethlehem, PA 18015 USA; 5.Univ Kansas, Dept Chem, Lawrence, KS 66045 USA; 6.Univ Chicago, Dept Biochem & Mol Biol, 920 E 58Th St, Chicago, IL 60637 USA; 7.Univ Maryland, Sch Pharm, Dept Pharmaceut Sci, Baltimore, MD 21201 USA; 8.Univ Maryland, Dept Chem & Biomol Engn, Baltimore, MD 21201 USA; 9.Univ Maryland, Biophys Program, Baltimore, MD 21201 USA
推荐引用方式 GB/T 7714	Jo, Sunhwan,Cheng, Xi,Lee, Jumin,et al. CHARMM-GUI 10 years for biomolecular modeling and simulation[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY,2017,38(15):1114-1124.
APA	Jo, Sunhwan.,Cheng, Xi.,Lee, Jumin.,Kim, Seonghoon.,Park, Sang-Jun.,...&Im, Wonpil.(2017).CHARMM-GUI 10 years for biomolecular modeling and simulation.JOURNAL OF COMPUTATIONAL CHEMISTRY,38(15),1114-1124.
MLA	Jo, Sunhwan,et al."CHARMM-GUI 10 years for biomolecular modeling and simulation".JOURNAL OF COMPUTATIONAL CHEMISTRY 38.15(2017):1114-1124.