Force fields for homology modeling

Andrew J. Bordner

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)

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 publicationMethods in Molecular Biology
Pages83-106
Number of pages24
Volume857
DOIs
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
Volume857
ISSN (Print)10643745

Fingerprint

Proteins
Physics
Membranes

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

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

Force fields for homology modeling. / Bordner, Andrew J.

Methods in Molecular Biology. Vol. 857 2012. p. 83-106 (Methods in Molecular Biology; Vol. 857).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bordner, AJ 2012, Force fields for homology modeling. in Methods in Molecular Biology. vol. 857, Methods in Molecular Biology, vol. 857, pp. 83-106. https://doi.org/10.1007/978-1-61779-588-6_4
Bordner AJ. Force fields for homology modeling. In Methods in Molecular Biology. Vol. 857. 2012. p. 83-106. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-588-6_4
Bordner, Andrew J. / Force fields for homology modeling. Methods in Molecular Biology. Vol. 857 2012. pp. 83-106 (Methods in Molecular Biology).
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