MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

被引：3304

作者：

Miller, Bill R., III ^{[1
]}

McGee, T. Dwight, Jr. ^{[1
]}

Swails, Jason M. ^{[1
]}

Homeyer, Nadine ^{[2
]}

Gohlke, Holger ^{[2
]}

Roitberg, Adrian E. ^{[1
]}

机构：

[1] Univ Florida, Dept Chem, Quantum Theory Project, Gainesville, FL 32611 USA

[2] Univ Dusseldorf, Dept Math & Nat Sci, Inst Pharmaceut & Med Chem, D-40225 Dusseldorf, Germany

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2012年 / 8卷 / 09期

基金：

美国国家科学基金会;

关键词：

MOLECULAR-MECHANICS; CONTINUUM SOLVENT; BINDING; DOCKING; QM/MM; DNA;

D O I：

10.1021/ct300418h

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.

引用

页码：3314 / 3321

页数：8

共 37 条

[1]

[Anonymous], 2014, AMBER

[2] Electrostatics of nanosystems: Application to microtubules and the ribosome [J].

Baker, NA ;

Sept, D ;

Joseph, S ;

Holst, MJ ;

McCammon, JA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (18) :10037-10041

[3] HARMONIC-ANALYSIS OF LARGE SYSTEMS .1. METHODOLOGY [J].

BROOKS, BR ;

JANEZIC, D ;

KARPLUS, M .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (12) :1522-1542

[4] Free energy calculations of protein-ligand interactions [J].

de Ruiter, Anita ;

Oostenbrink, Chris .

CURRENT OPINION IN CHEMICAL BIOLOGY, 2011, 15 (04) :547-552

[5] GROUND-STATES OF MOLECULES .38. MNDO METHOD - APPROXIMATIONS AND PARAMETERS [J].

DEWAR, MJS ;

THIEL, W .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1977, 99 (15) :4899-4907

[6] THE DEVELOPMENT AND USE OF QUANTUM-MECHANICAL MOLECULAR-MODELS .76. AM1 - A NEW GENERAL-PURPOSE QUANTUM-MECHANICAL MOLECULAR-MODEL [J].

DEWAR, MJS ;

ZOEBISCH, EG ;

HEALY, EF ;

STEWART, JJP .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1985, 107 (13) :3902-3909

[7] An MM/3D-RISM Approach for Ligand Binding Affinities [J].

Genheden, Samuel ;

Luchko, Tyler ;

Gusarov, Sergey ;

Kovalenko, Andriy ;

Ryde, Ulf .

JOURNAL OF PHYSICAL CHEMISTRY B, 2010, 114 (25) :8505-8516

[8] How to Obtain Statistically Converged MM/GBSA Results [J].

Genheden, Samuel ;

Ryde, Ulf .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2010, 31 (04) :837-846

[9] QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors [J].

Gleeson, M. Paul ;

Gleeson, Duangkamol .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2009, 49 (06) :1437-1448

[10] Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RaIGDS complexes [J].

Gohlke, H ;

Kiel, C ;

Case, DA .

JOURNAL OF MOLECULAR BIOLOGY, 2003, 330 (04) :891-913

← 1 2 3 4 →