Using DelPhi to compute electrostatic potentials and assess their contribution to interactions

Current Protocols in Bioinformatics
Assaf OronRuth Nussinov

Abstract

There is a general agreement that electrostatic interactions play a significant role in the structure and function of biological molecules. However, obtaining quantitative estimation of the electrostatic energy requires computational models that capture the microscopic nature of the heterogeneous environment of macromolecules. This protocol offers elaboration on one of the common methods to calculate the electrostatic energetic contributions using continuum electrostatics. The method involves solving the Poisson-Boltzmann (PB) equation numerically and regarding the solute as having a homogenous dielectric constant. In order to apply this method, a three dimensional structure of the molecule derived from experimental data (crystallography, NMR) or modeling techniques is required. The protocol will focus on the DelPhi program (Accelrys Inc. San Diego), which is one of the most common programs used for the estimation of electrostatic free energy contribution. A simple procedure of assigning criteria and parameters (charge distribution, solvent and solute dielectric constants, iterations, grid resolution, etc) enables one to illustrate an electrostatic potential map and estimate the electrostatic free energy, although with limited ...Continue Reading

References

Jan 1, 1991·Methods in Enzymology·T P Straatsma, J A McCammon
Jan 1, 1988·Proteins·M K Gilson, B H Honig
Oct 23, 1987·Science·J A McCammon
Nov 1, 1986·Biopolymers·M K Gilson, B H Honig
Dec 1, 1984·Journal of Medicinal Chemistry·P R AndrewsJ L Martin
Dec 22, 1995·Journal of Medicinal Chemistry· Ajay, M A Murcko
Jun 1, 1997·Protein Science : a Publication of the Protein Society·N FroloffB Honig
Sep 2, 1999·Protein Engineering·J E NielsenR C Wade
Apr 8, 2000·Current Opinion in Structural Biology·F B SheinermanB Honig
Apr 12, 2001·Current Opinion in Structural Biology·D J Tobias

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Citations

May 17, 2011·Physical Biology·Zhe ZhangEmil Alexov
Mar 27, 2012·Journal of Bacteriology·Subramaniapillai KolappanLisa Craig
Feb 23, 2012·Scientific Reports·Ramachandra M Bhaskara, Narayanaswamy Srinivasan
Apr 15, 2015·Nucleic Acids Research·Xiangqian KongCheng Luo
Jul 25, 2019·Frontiers in Molecular Biosciences·Geraldo Rodrigues Sartori, Alessandro S Nascimento
Sep 1, 2019·The Journal of Biological Chemistry·Miguel Gutierrez-RodarteLisa Craig

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