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

作　　者：Subhra Sarkar Shawn Witham Jie Zhang Maxim Zhenirovskyy Walter Rocchia Emil Alexov 

机构地区：[1]Computational Biophysics and Bioinformatics,Department of Physics,Clemson University,Clemson,SC 29634,USA [2]Department of Computer Science,Clemson University,Clemson,SC 29634,USA [3]Drug Discovery and Development,Italian Institute of Technology,via Morego 30,16163 Genova,Italy

出　　处：《Communications in Computational Physics》2013年第1期269-284,共16页计算物理通讯（英文）

基　　金：supported by a grant from the Institute of General Medical Sciences,National Institutes of Health,award number 1R01GM093937.

摘　　要：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.

关 键 词：DELPHI ELECTROSTATICS proteins continuum models electrostatic potential finitedifference Poisson-Boltzmann solver 

分 类 号：TP3[自动化与计算机技术—计算机科学与技术]