Accuracy assessment of semiempirical molecular electrostatic potential of proteins

Victor Anisimov, Nikolay Anikin, Vladislav Bugaenko, Vladimir Bobrikov, Alexey Andreyev

Research output: Contribution to journalArticlepeer-review

Abstract

Accurate electrostatic maps of proteins are of great importance in research of protein interaction with ligands, solvent media, drugs, and other biomolecules. The large size of real-life proteins imposes severe limitations on computational methods one can use for obtaining the electrostatic map. Well-known accurate second-order Møller-Plesset and density functional theory methods are not routinely applicable to systems larger than several hundred atoms. Conventional semi-empirical tools, as less resource demanding ones, could be an attractive solution but they do not yield sufficiently accurate calculation results with reference to protein systems, as our analysis demonstrates. The present work performs a thorough analysis of the accuracy issues of the modified neglect of differential overlap type semi-empirical Hamiltonians AM1 and PM3 on example of the calculation of the molecular electrostatic potential and the dipole moment of natural amino acids. Real capabilities and limitations of these methods with application to protein modeling are discussed.

Original languageEnglish (US)
Pages (from-to)213-219
Number of pages7
JournalTheoretical Chemistry Accounts
Volume109
Issue number4
DOIs
StatePublished - May 1 2003
Externally publishedYes

Keywords

  • Biomolecules
  • Coulomb potential
  • Dipole moment
  • Electrostatic maps
  • Semiempirical method

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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