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. 2011 May;32(7):1488-91.
doi: 10.1002/jcc.21720. Epub 2011 Feb 1.

Web servers and services for electrostatics calculations with APBS and PDB2PQR

Web servers and services for electrostatics calculations with APBS and PDB2PQR

Samir Unni et al. J Comput Chem. 2011 May.

Abstract

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/.

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Figures

Figure 1
Figure 1
An overview of how users can interact with APBS Web services either through the standalone client or through the PDB2PQR web server. The web server offers the additional benefit of Jmol visualization without the requirement for additional software installation.

References

    1. Dong F, Olsen B, Baker NA. Computational methods for biomolecular electrostatics. Methods Cell Biol. 2008;84:843–870. - PMC - PubMed
    1. Grochowski P, Trylska J. Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications. Biopolymers. 2008;89:93–113. - PubMed
    1. World Wide Web Consortium. Web Services Description Language (WSDL) 1.1. 2010.
    1. Krishnan S, Clementi L, Ren J, Papadopoulos P, Li W. Design and Evaluation of Opal2: A Toolkit for Scientific Software as a Service. 2009 IEEE Congress on Services (SERVICES-1 2009) 2009
    1. Ren J, Williams N, Clementi L, Krishnan S, Li WW. Opal web services for biomedical applications. Nucleic Acids Res. 2010;38 Suppl:W724–W731. - PMC - PubMed

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