title: DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.
abstract: A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions.
  
  
  METHODS
  The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhi software. The computation is carried out on supercomputer cluster and results are given back to the user via http protocol, including the ability to visualize the structure and corresponding electrostatic potential via Jmol implementation. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.
authors.affiliation: Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA. nsmith@clemson.edu
authors.forename: Nicholas
authors.initials: N
authors.lastname: Smith
authors.forename: Shawn
authors.initials: S
authors.lastname: Witham
authors.forename: Subhra
authors.initials: S
authors.lastname: Sarkar
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.forename: Chuan
authors.initials: C
authors.lastname: Li
authors.forename: Emil
authors.initials: E
authors.lastname: Alexov
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020407:Internet; D008958:Models, Molecular; D049329:Nanostructures / Q000032:analysis; D012984:Software; D055672:Static Electricity; D014584:User-Computer Interface