CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues

被引：266

作者：

Jo, Sunhwan ^{[1
]}

Cheng, Xi ^{[2
,3
]}

Islam, Shahidul M. ^{[1
]}

Huang, Lei ^{[1
]}

Rui, Huan ^{[1
]}

Zhu, Allen ^{[1
]}

Lee, Hui Sun ^{[2
,3
]}

Qi, Yifei ^{[2
,3
]}

Han, Wei ^{[4
,5
]}

Vanommeslaeghe, Kenno ^{[6
]}

MacKerell, Alexander D., Jr. ^{[6
]}

Roux, Benoit ^{[1
]}

Im, Wonpil ^{[2
,3
]}

机构：

[1] Univ Chicago, Dept Biochem & Mol Biol, Gordon Ctr Integrat Sci, Chicago, IL 60637 USA

[2] Univ Kansas, Dept Mol Biosci, Lawrence, KS 66045 USA

[3] Univ Kansas, Ctr Bioinformat, Lawrence, KS 66045 USA

[4] Univ Illinois, Beckman Inst, Urbana, IL 61801 USA

[5] Univ Illinois, Ctr Biophys & Computat Biol, Urbana, IL 61801 USA

[6] Univ Maryland, Sch Pharm, Dept Pharmaceut Sci, Baltimore, MD 21201 USA

来源：

BIOMOLECULAR MODELLING AND SIMULATIONS | 2014年 / 96卷

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; SPIN-LABELED PROTEINS; GENERAL FORCE-FIELD; CLASSICAL DRUDE OSCILLATOR; FREE-ENERGY CALCULATIONS; UNNATURAL AMINO-ACIDS; T4; LYSOZYME; BIOMOLECULAR SIMULATION; NITROXIDE MOTION; SIDE-CHAIN;

D O I：

10.1016/bs.apcsb.2014.06.002

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

CHARMM-GUI, http:/www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins.

引用

页码：235 / 265

页数：31

共 92 条

[1] CONFORMATIONAL-ANALYSIS .130. MM2 - HYDROCARBON FORCE-FIELD UTILIZING V1 AND V2 TORSIONAL TERMS [J].

ALLINGER, NL .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1977, 99 (25) :8127-8134

[2] Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds [J].

Allinger, NL ;

Chen, KH ;

Lii, JH ;

Durkin, KA .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2003, 24 (12) :1447-1472

[3] MOLECULAR MECHANICS - THE MM3 FORCE-FIELD FOR HYDROCARBONS .1. [J].

ALLINGER, NL ;

YUH, YH ;

LII, JH .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1989, 111 (23) :8551-8566

[4]

[Anonymous], 2010, The PyMOL Molecular Graphics System (2.5.4)

[5] A NOVEL REVERSIBLE THIOL-SPECIFIC SPIN LABEL - PAPAIN ACTIVE-SITE LABELING AND INHIBITION [J].

BERLINER, LJ ;

GRUNWALD, J ;

HANKOVSZKY, HO ;

HIDEG, K .

ANALYTICAL BIOCHEMISTRY, 1982, 119 (02) :450-455

[6] Energetics of ion conduction through the K+ channel [J].

Bernèche, S ;

Roux, B .

NATURE, 2001, 414 (6859) :73-77

[7] Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles [J].

Best, Robert B. ;

Zhu, Xiao ;

Shim, Jihyun ;

Lopes, Pedro E. M. ;

Mittal, Jeetain ;

Feig, Michael ;

MacKerell, Alexander D., Jr. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (09) :3257-3273

[8]

Bohacek RS, 1996, MED RES REV, V16, P3, DOI 10.1002/(SICI)1098-1128(199601)16:1<3::AID-MED1>3.0.CO

[9]

2-6

[10] CHARMM: The Biomolecular Simulation Program [J].

Brooks, B. R. ;

Brooks, C. L., III ;

Mackerell, A. D., Jr. ;

Nilsson, L. ;

Petrella, R. J. ;

Roux, B. ;

Won, Y. ;

Archontis, G. ;

Bartels, C. ;

Boresch, S. ;

Caflisch, A. ;

Caves, L. ;

Cui, Q. ;

Dinner, A. R. ;

Feig, M. ;

Fischer, S. ;

Gao, J. ;

Hodoscek, M. ;

Im, W. ;

Kuczera, K. ;

Lazaridis, T. ;

Ma, J. ;

Ovchinnikov, V. ;

Paci, E. ;

Pastor, R. W. ;

Post, C. B. ;

Pu, J. Z. ;

Schaefer, M. ;

Tidor, B. ;

Venable, R. M. ;

Woodcock, H. L. ;

Wu, X. ;

Yang, W. ;

York, D. M. ;

Karplus, M. .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (10) :1545-1614

← 1 2 3 4 5 6 7 8 9 10 →