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DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes

Published online by Cambridge University Press:  03 June 2015

Subhra Sarkar,
Shawn Witham,
Jie Zhang,
Maxim Zhenirovskyy,
Walter Rocchia and
Emil Alexov
Subhra Sarkar
Affiliation:
Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USADepartment of Computer Science, Clemson University, Clemson, SC 29634, USA
Shawn Witham*
Affiliation:
Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
Jie Zhang*
Affiliation:
Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USADepartment of Computer Science, Clemson University, Clemson, SC 29634, USA
Maxim Zhenirovskyy*
Affiliation:
Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
Walter Rocchia*
Affiliation:
Drug Discovery and Development, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy
Emil Alexov*
Affiliation:
Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
*
Email:switham@clemson.edu
Email:zhangjie190@gmail.com
Email:mzhenir@clemson.edu
Email:Walter.Rocchia@iit.it
Corresponding author.Email:ealexov@clemson.edu
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Abstract

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Keywords

82.20.WtDelPhielectrostaticsproteinscontinuum modelselectrostatic potentialfinite-difference Poisson-Boltzmann solver

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Type
Research Article
Information
Communications in Computational Physics , Volume 13 , Issue 1 , January 2013, pp. 269 - 284
Copyright
Copyright © Global Science Press Limited 2013

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