Computational Biophysics and Bioinformatics

Professor Emil Alexov Group


DelPhi Software Management and Development
Supported by a grant from NIGMS, NIH, grant number: R01 GM093937 and R35 GM151964

One of the main problems in modeling the electrostatic potential of biological macromolecules is that they exist in water at a given ionic strength and that they have an irregular shape. Analytical solutions of the corresponding Poisson-Boltzmann Equation (PBE) are not available for such cases and the distribution of the potential can be found only numerically. DelPhi, developed in Professor Barry Honig's lab in 1986, was the first PBE solver used by many researchers. The widespread popularity of DelPhi is due to its speed, accuracy (calculation of the electrostatic free energy is only slightly dependent on the resolution of the grid) and the ability to handle extremely high grid dimensions (more than 1,000 x 1,000 x 1,000). Current version comes with OpenMP and MPI options and distributed memory. Additional features such as assigning different dielectric constants to different regions of space (Fortran version), Gaussian-based smooth dielectric function, calculating Zeta-potential, modeling salt via modified Boltzmann factor and without sharp border between solute-solvent also attracted many researchers. In addition to the typical potential map, DelPhi can generate and output the calculated distribution of either the dielectric constant or ion concentration, providing the biomedical community with extra tools for their research. New tools include DelPhiPKa, DelPhiForce. BION and tools for mutational analysis. DelPhi is maintained and developed by the "DelPhi Development Team" at Clemson University. Delphi reference papers can be found here: papers. Please refer to our Wikipedia page for more help.

Delphi Tutorial

The text of this page is available for modification and reuse under the terms of the Creative Commons Attribution-Sharealike 3.0 Unported License.
Remember to cite these papers when using Delphi for your own research publications.
Please cite the following paper when publishing anything resulting from usage of our downloadable DelPhi distribution:
  • Li C, Jia Z, Chakravorty A, Pahari S, Peng Y, Basu S, Koirala M, Panday SK, Petukh M, Li L, Alexov E. "DelPhi Suite: New Developments and Review of Functionalities." , J Comput Chem. 2019 Oct 30;40(28):2502-2508. doi: 10.1002/jcc.26006. Epub 2019 Jun 25.
  • Li L, Li C, Sarkar S, Zhang J, Witham S, Zhang Z, Wang L, Smith N, Petukh M, Alexov E. "DelPhi: a comprehensive suite for DelPhi software and associated resources." BMC Biophys, (2012) May14;4(1):9.
  • Usage of parallelized DelPhi should be acknowledged by citing the following: Li C, Li L, Zhang J, Alexov E., "Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi.", J Comput Chem. 2012 Sep 15;33(24):1960-6.
  • Continuous development of schemes for parallel computing of the electrostatics in biological systems: implementation in DelPhi. Li C, Petukh M, Li L, Alexov E. J Comput Chem. 2013 Aug 15;34(22):1949-60.
Please cite the following papers when publishing anything resulting from usage of our DelPhi web-server:
  • Smith N, Witham S, Sarkar S, Zhang J, Li L, Li C, Alexov E. "DelPhi Web Server v2: Incorporating atomic-style geometrical figures into the computational protocol", Bioinformatics 2012 Jun 15;28(12):1655-7. Epub 2012 Apr 23.
  • Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia and Emil Alexov "DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes", Comm. Comp. Phys., (2013), 13, 269-84
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