期刊
COMMUNICATIONS IN COMPUTATIONAL PHYSICS
卷 13, 期 1, 页码 269-284出版社
GLOBAL SCIENCE PRESS
DOI: 10.4208/cicp.300611.201011s
关键词
DelPhi; electrostatics; proteins; continuum models; electrostatic potential; finite-difference Poisson-Boltzmann solver
资金
- Institute of General Medical Sciences, National Institutes of Health [1R01GM093937]
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM093937] Funding Source: NIH RePORTER
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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