AI Article Synopsis
- Accurate modeling of electrostatic potential is crucial for studying biological macromolecules, but it's challenging due to their irregular shapes and the presence of water and ions.
- The DelPhi solver has been enhanced with new features to make it easier for users to download and install, including executables, source code, and a manual.
- The DelPhi suite provides not just resources and examples for users, but also a forum for collaboration and support, all available for free to academic users.
Article 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.
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|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463482 | PMC |
| http://dx.doi.org/10.1186/2046-1682-5-9 | DOI Listing |
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