Portal de Periódicos da CAPES

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol

2012; Oxford University Press; Volume: 28; Issue: 12 Linguagem: Inglês

10.1093/bioinformatics/bts200

1367-4811

Nicholas Smith, Shawn Witham, Subhra Sarkar, Jie Zhang, Lin Li, Chuan Li, Emil Alexov,

Algorithms and Data Compression

Abstract Summary: 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. Availability and implementation: 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. Contact: nsmith@clemson.edu, ealexov@clemson.edu Supplementary information: Supplementary data are available at Bioinformatics online.