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Web servers and services for electrostatics calculations with APBS and PDB2PQR
Author(s) -
Unni Samir,
Huang Yong,
Hanson Robert M.,
Tobias Malcolm,
Krishnan Sriram,
Li Wilfred W.,
Nielsen Jens E.,
Baker Nathan A.
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21720
Subject(s) - scalability , software , computer science , electrostatics , web application , interface (matter) , server , web server , range (aeronautics) , web service , visualization , computational science , user interface , world wide web , the internet , operating system , data mining , materials science , chemistry , bubble , maximum bubble pressure method , composite material
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/.