Web servers and services for electrostatics calculations with APBS and PDB2PQR

Samir Unni, Yong Huang, Robert M. Hanson, Malcolm Tobias, Sriram Krishnan, Wilfred W. Li, Jens E. Nielsen, Nathan A. Baker

Research output: Contribution to journalArticle

141 Scopus citations

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:. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

Original languageEnglish
Pages (from-to)1488-1491
Number of pages4
JournalJournal of Computational Chemistry
Volume32
Issue number7
DOIs
StatePublished - May 1 2011

Keywords

  • electrostatics
  • salvation
  • web server
  • web services

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    Unni, S., Huang, Y., Hanson, R. M., Tobias, M., Krishnan, S., Li, W. W., Nielsen, J. E., & Baker, N. A. (2011). Web servers and services for electrostatics calculations with APBS and PDB2PQR. Journal of Computational Chemistry, 32(7), 1488-1491. https://doi.org/10.1002/jcc.21720