DelPhi: a comprehensive suite for DelPhi software and associated resources.

BMC Biophysics
Lin LiEmil Alexov

Abstract

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions. Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding investigation. Non-experienced researchers can download examples containing all necessary data to carry out DelPhi runs on a set of selected examples illustrating various DelPhi features and demonstrating DelPhi's accuracy against analytical solutions. DelPhi suite offers not only the DelPhi executable and sources files, examples and parameter files, but also provides links to third party developed resources either utilizing DelPhi or providing plugins for DelPhi. In addition, the users and developers are offered a forum to share ideas, resolve issues, report ...Continue Reading

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Citations

Mar 8, 2013·PLoS Computational Biology·Zhe ZhangEmil Alexov
Sep 27, 2013·PloS One·Zheng XuJiahai Zhou
May 21, 2014·Computational Biology and Chemistry·Rehan Zafar ParachaSyed Aun Muhammad
May 6, 2014·Bioinformatics·Praveen Nedumpully-GovindanFeng Ding
Oct 18, 2014·Nucleic Acids Research·Arnab Bhattacherjee, Yaakov Levy
Feb 6, 2013·Bioinformatics·Marharyta PetukhEmil Alexov
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Methods Mentioned

BETA
protein folding
protein

Software Mentioned

Linux
CHARMM
APBS
OPLS
AMBER98
Mac
MEAD
PARSE
ZAP
Biskit

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