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Open Access Highly Accessed Software

DelPhi: a comprehensive suite for DelPhi software and associated resources

Lin Li1, Chuan Li1, Subhra Sarkar12, Jie Zhang12, Shawn Witham1, Zhe Zhang1, Lin Wang1, Nicholas Smith1, Marharyta Petukh1 and Emil Alexov1*

Author affiliations

1 Physics Department, Computational Biophysics and Bioinformatics, Clemson University, Clemson, SC, 29642, USA

2 Department of Computer Science, Clemson University, Clemson, SC, 29642, USA

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Citation and License

BMC Biophysics 2012, 5:9  doi:10.1186/2046-1682-5-9

Published: 14 May 2012

Abstract

Background

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.

Results

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.

Conclusions

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 bugs and seek help with respect to the DelPhi package. The resource is available free of charge for academic users from URL: http://compbio.clemson.edu/DelPhi.php. webcite

Keywords:
DelPhi; Poisson-Boltzmann equation; Implicit solvation model; Electrostatics; Biological macromolecules; Software