Commun. Comput. Phys., 13 (2013), pp. 269-284.


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

Subhra Sarkar 1, Shawn Witham 2, Jie Zhang 1, Maxim Zhenirovskyy 2, Walter Rocchia 3, Emil Alexov 2*

1 Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA; and Department of Computer Science, Clemson University, Clemson, SC 29634, USA.
2 Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA.
3 Drug Discovery and Development, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy.

Received 30 June 2011; Accepted (in revised version) 20 October 2011
Available online 12 June 2012
doi:10.4208/cicp.300611.201011s

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.


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PACS: 82.20.Wt
Key words: DelPhi, electrostatics, proteins, continuum models, electrostatic potential, finite-difference Poisson-Boltzmann solver.

*Corresponding author.
Email: switham@clemson.edu (S. Witham), zhangjie190@gmail.com (J. Zhang), mzhenir@clemson.edu (M. Zhenirovskyy), Walter.Rocchia@iit.it (W. Rocchia), ealexov@clemson.edu (E. Alexov)
 

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