LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

被引：1160

作者：

Dodda, Leela S. ^{[1
]}

de Vaca, Israel Cabeza ^{[1
]}

Tirado-Rives, Julian ^{[1
]}

Jorgensen, William L. ^{[1
]}

机构：

[1] Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA

来源：

NUCLEIC ACIDS RESEARCH | 2017年 / 45卷 / W1期

基金：

美国国家卫生研究院;

关键词：

SOLVATION FREE-ENERGIES; FORCE-FIELD; POTENTIAL FUNCTIONS; MOLECULAR-DYNAMICS; PARTIAL CHARGES; ATOMIC CHARGES; CHARMM; SIMULATION; MODEL; ENERGETICS;

D O I：

10.1093/nar/gkx312

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：

The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements.

引用

页码：W331 / W336

页数：6

共 42 条

[21] Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids [J].

Jorgensen, WL ;

Maxwell, DS ;

TiradoRives, J .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, 118 (45) :11225-11236

[22] THE OPLS POTENTIAL FUNCTIONS FOR PROTEINS - ENERGY MINIMIZATIONS FOR CRYSTALS OF CYCLIC-PEPTIDES AND CRAMBIN [J].

JORGENSEN, WL ;

TIRADORIVES, J .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1988, 110 (06) :1657-1666

[23] SM6: A density functional theory continuum solvation model for calculating aqueous solvation free energies of neutrals, ions, and solute-water clusters [J].

Kelly, CP ;

Cramer, CJ ;

Truhlar, DG .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2005, 1 (06) :1133-1152

[24] New class IV charge model for extracting accurate partial charges from wave functions [J].

Li, JB ;

Zhu, TH ;

Cramer, CJ ;

Truhlar, DG .

JOURNAL OF PHYSICAL CHEMISTRY A, 1998, 102 (10) :1820-1831

[25] A Toolkit for the Analysis of Free-Energy Perturbation Calculations [J].

Liu, Peng ;

Dehez, Francois ;

Cai, Wensheng ;

Chipot, Christophe .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (08) :2606-2616

[26] Self-consistent reaction field model for aqueous and nonaqueous solutions based on accurate polarized partial charges [J].

Marenich, Aleksandr V. ;

Olson, Ryan M. ;

Kelly, Casey P. ;

Cramer, Christopher J. ;

Truhlar, Donald G. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2007, 3 (06) :2011-2033

[27] Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases [J].

Marenich, Aleksandr V. ;

Jerome, Steven V. ;

Cramer, Christopher J. ;

Truhlar, Donald G. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (02) :527-541

[28] CHARMMing: A new, flexible web portal for CHARMM [J].

Miller, Benjamin T. ;

Singh, Rishi P. ;

Klauda, Jeffery B. ;

Hodoscek, Milan ;

Brooks, Bernard R. ;

Woodcock, H. Lee, III .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2008, 48 (09) :1920-1929

[29] Scalable molecular dynamics with NAMD [J].

Phillips, JC ;

Braun, R ;

Wang, W ;

Gumbart, J ;

Tajkhorshid, E ;

Villa, E ;

Chipot, C ;

Skeel, RD ;

Kalé, L ;

Schulten, K .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1781-1802

[30] OPLS POTENTIAL FUNCTIONS FOR NUCLEOTIDE BASES - RELATIVE ASSOCIATION CONSTANTS OF HYDROGEN-BONDED BASE-PAIRS IN CHLOROFORM [J].

PRANATA, J ;

WIERSCHKE, SG ;

JORGENSEN, WL .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1991, 113 (08) :2810-2819

← 1 2 3 4 5 →