Web Servers and Services for Electrostatics Calculations with APBS and PDB2PQR

被引：239

作者：

Unni, Samir ^{[2
]}

Huang, Yong ^{[2
]}

Hanson, Robert M. ^{[3
]}

Tobias, Malcolm ^{[2
]}

Krishnan, Sriram ^{[4
]}

Li, Wilfred W. ^{[4
]}

Nielsen, Jens E. ^{[5
]}

Baker, Nathan A. ^{[1
]}

机构：

[1] Pacific NW Natl Lab, Div Computat & Stat Analyt, Richland, WA 99352 USA

[2] Washington Univ, Ctr Computat Biol, St Louis, MO USA

[3] St Olaf Coll, Dept Chem, Northfield, MN 55057 USA

[4] Univ Calif San Diego, Natl Biomed Computat Resource, San Diego, CA 92103 USA

[5] Univ Coll Dublin, Sch Biomol & Biomed Sci, Dublin 2, Ireland

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2011年 / 32卷 / 07期

关键词：

electrostatics; salvation; web server; web services;

D O I：

10.1002/jcc.21720

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 1488-1491, 2011

引用

页码：1488 / 1491

页数：4

共 12 条

[1]

[Anonymous], WEB SERV DESCR LANG

[2]

[Anonymous], 2010, Jmol: an open-source Java viewer for chemical structures in 3D

[3]

[Anonymous], 2009 IEEE C SERV SER

[4] 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

[5]

DeLano W.L., 2002, The PyMOL molecular graphics system

[6] PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations [J].

Dolinsky, TJ ;

Nielsen, JE ;

McCammon, JA ;

Baker, NA .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W665-W667

[7] PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations [J].

Dolinsky, Todd J. ;

Czodrowski, Paul ;

Li, Hui ;

Nielsen, Jens E. ;

Jensen, Jan H. ;

Klebe, Gerhard ;

Baker, Nathan A. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W522-W525

[8] Computational methods for biomolecular electrostatics [J].

Dong, Feng ;

Olsen, Brett ;

Baker, Nathan A. .

BIOPHYSICAL TOOLS FOR BIOLOGISTS: VOL 1 IN VITRO TECHNIQUES, 2008, 84 :843-+

[9] Review: Continuum molecular electrostatics, salt effects, and counterion binding-a review of the Poisson-Boltzmann theory and its modifications [J].

Grochowski, Pawel ;

Trylska, Joanna .

BIOPOLYMERS, 2008, 89 (02) :93-113

[10] VMD: Visual molecular dynamics [J].

Humphrey, W ;

Dalke, A ;

Schulten, K .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1996, 14 (01) :33-38

← 1 2 →