DelPhi: a comprehensive suite for DelPhi software and associated resources

By Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, N. Smith, M. Petukh, Emil Alexov. BMC Biophysics, 2012

353 citations recorded by the source corpus.

BackgroundAccurate 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.ResultsHere 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.ConclusionsDelPhi 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

Subfields: Biomedical Engineering, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/d06e81f27a181b7bbae51d5e6f4ae62924087f53

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In Biomedical Engineering

1. T. Head‐Gordon
2. G. Wei
3. Aleksei Aksimentiev
4. Ö. Civalek
5. Yang Xiang
6. Sining Yu

In Molecular Biology

1. Sunghwan Kim
2. Evan E. Bolton
3. Thomas L. Madden
4. Nathan A. Baker
5. James Andrew McCammon
6. Jiyao Wang
7. Jens Erik Nielsen
8. Todd J. Dolinsky

In Spectroscopy

1. Evan E. Bolton
2. Sunghwan Kim
3. Aron Marchler-Bauer
4. David Ryan Koes
5. Thomas L. Madden
6. Stephen H. Bryant
7. Bo Yu
8. Lianyi Han

Citations in the corpus

• Improvements to the APBS biomolecular solvation software suite (2017, background): “The most significant (based on user base and citations) of these include CHARMM [12], AMBER [13], DelPhi [14], Jaguar [15], Zap [16], MIBPB [17], and APBS [18].”
• Database resources of the National Center for Biotechnology Information (2020, methodology): “…features include extended visualization of 2D interaction networks between proteins and ligands or other proteins, visualization of electrostatic potentials as computed by Delphi (21) and visualization of membrane bilayer location relative to membrane protein structures as provided by OPM (22).”
• The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study (2016, background): “Continuum electrostatic calculations [18] elucidated the electrostatic interaction between the hinge region and DNA and its dependence on the salt concentration.”