Force fields for homology modeling

Andrew J. Bordner

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Scopus citations

Abstract

Accurate all-atom energy functions are crucial for successful high-resolution protein structure prediction. In this chapter, we review both physics-based force fields and knowledge-based potentials used in protein modeling. Because it is important to calculate the energy as accurately as possible given the limitations imposed by sampling convergence, different components of the energy, and force fields representing them to varying degrees of detail and complexity are discussed. Force fields using Cartesian as well as torsion angle representations of protein geometry are covered. Since solvent is important for protein energetics, different aqueous and membrane solvation models for protein simulations are also described. Finally, we summarize recent progress in protein structure refinement using new force fields.

Original languageEnglish (US)
Title of host publicationHomology Modeling
Subtitle of host publicationMethods and Protocols
EditorsAndrew Orry, Ruben Abagyan
Pages83-106
Number of pages24
DOIs
StatePublished - Mar 16 2012

Publication series

NameMethods in Molecular Biology
Volume857
ISSN (Print)1064-3745

Keywords

  • Force field
  • Homology modeling
  • Implicit solvation
  • Knowledge-based potential
  • Protein structure refinement

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Bordner, A. J. (2012). Force fields for homology modeling. In A. Orry, & R. Abagyan (Eds.), Homology Modeling: Methods and Protocols (pp. 83-106). (Methods in Molecular Biology; Vol. 857). https://doi.org/10.1007/978-1-61779-588-6_4