Protein electrostatics on personal computers

György G. Ferenczy, János G. Ángyán, Tibor Koritsánszky, Jenö Nagy, Gábor Náray-Szabó

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

A computer program for the IBM PC series allowing the simple treatment of protein electrostatics is presented. It is based on the Bond Increment method for the calculation of molecular electrostatic potentials and generates input from Protein Data Bank files. Calculated electrostatic potentials for small model molecules with and without the application of orthogonalized atomic hybrid orbitals are compared to ab initio ones obtained with the 4-31G basis set, and a fair linear correlation found between values from both calculations. Another test of the method is the estimation of binding energies between native and mutant trypsin and some tetrapeptide substrates. Our approximate binding energies show good correlation with experimental values and with values obtained from the protein dipoles langevin dipoles method. With an appropriate linear correction, the method outlined here calculates electrostatic potentials near proteins relatively close to the ab initio values, both at small and large distances from the molecule. This feature seems to make it superior to others making use of atomic monopoles in the calculation.

Original languageEnglish
Pages (from-to)113-123
Number of pages11
JournalJournal of Molecular Structure: THEOCHEM
Volume256
Issue numberC
DOIs
Publication statusPublished - Apr 23 1992

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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