Web servers and services for electrostatics calculations with APBS and PDB2PQR

By Samir Unni, Yong Huang, Robert M. Hanson, M. Tobias, S. Krishnan, Wilfred W. Li, Jens Erik Nielsen, Nathan A. Baker. Journal of Computational Chemistry, 2011

304 citations recorded by the source corpus.

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

Subfields: Biomedical Engineering, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1d09bd11c2465f59a4d0335f548869fdeaf35781

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In Biomedical Engineering

  1. T. Head‐Gordon
  2. G. Wei
  3. Ö. Civalek
  4. Yang Xiang
  5. Sining Yu

In Materials Chemistry

  1. T. Head‐Gordon
  2. G. Wei
  3. David Ryan Koes
  4. Nathan A. Baker
  5. James Andrew McCammon
  6. Sean R. McGuffee
  7. Adrian H. Elcock

In Molecular Biology

  1. Nathan A. Baker
  2. James Andrew McCammon
  3. Jens Erik Nielsen
  4. Todd J. Dolinsky
  5. G. Wei
  6. David Ryan Koes
  7. David H. Brookes
  8. Sean R. McGuffee

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