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Logo of bmcbiophysBioMed CentralBiomed Central Web Sitesearchsubmit a manuscriptregisterthis articleBMC BiophysicsJournal Front Page
 
BMC Biophys. 2012; 5: 9.
Published online May 14, 2012. doi:  10.1186/2046-1682-5-9
PMCID: PMC3463482
DelPhi: a comprehensive suite for DelPhi software and associated resources
Reviewed by Lin Li,1 Chuan Li,1 Subhra Sarkar,1,2 Jie Zhang,1,2 Shawn Witham,1 Zhe Zhang,1 Lin Wang,1 Nicholas Smith,1 Marharyta Petukh,1 and Emil Alexovcorresponding author1
1Physics Department, Computational Biophysics and Bioinformatics, Clemson University, Clemson, SC, 29642, USA
2Department of Computer Science, Clemson University, Clemson, SC, 29642, USA
corresponding authorCorresponding author.
Lin Li: lli5/at/clemson.edu; Chuan Li: chuanli/at/clemson.edu; Subhra Sarkar: subhras/at/g.clemson.edu; Jie Zhang: jzhang8/at/clemson.edu; Shawn Witham: switham/at/clemson.edu; Zhe Zhang: zz/at/clemson.edu; Lin Wang: lwang3/at/clemson.edu; Nicholas Smith: nsmith/at/clemson.edu; Marharyta Petukh: mpetukh/at/clemson.edu; Emil Alexov: ealexov/at/clemson.edu
Received February 10, 2012; Accepted April 17, 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.
Keywords: DelPhi, Poisson-Boltzmann equation, Implicit solvation model, Electrostatics, Biological macromolecules, Software
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