Torsional relaxation for biopolymers

Wing Hung Wong, Yan Cui, Run Sheng Chen

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

We describe a method for making natural, physical movements in a chained polymer by sequentially adjusting a few neighboring torsion angles in the polymer backbone. In addition to being very fast and easy to implement, the method is also very general. It applies equally well to proteins and nucleic acids. This method is then used to design a local refinement procedure. We test the refinement procedure on the minimization of a simple energy function for proteins. The energy function has a simplified potential for hydrophobic interaction, a hydrogen-bond term, and a term for van der Waals interaction. There is considerable current interest in such simple energy functions for protein folding. When applied to refine structures found by a global search method, the refinement is able to produce large reduction in the hydrogen- bond term and the van der Waal term of the energy. We conclude that the method is particularly effective in finding good 'packing' of residues in an initially compact conformation.

Original languageEnglish (US)
Pages (from-to)655-665
Number of pages11
JournalJournal of Computational Biology
Volume5
Issue number4
DOIs
StatePublished - Jan 1 1998
Externally publishedYes

Fingerprint

Biopolymers
Energy Function
Hydrogen Bonds
Van Der Waals
Hydrogen bonds
Term
Proteins
Protein folding
Refinement
Polymers
Nucleic acids
Protein
Torsional stress
Local Refinement
Protein Folding
Conformations
Global Search
Backbone
Conformation
Interaction

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

Cite this

Torsional relaxation for biopolymers. / Wong, Wing Hung; Cui, Yan; Chen, Run Sheng.

In: Journal of Computational Biology, Vol. 5, No. 4, 01.01.1998, p. 655-665.

Research output: Contribution to journalArticle

Wong, Wing Hung ; Cui, Yan ; Chen, Run Sheng. / Torsional relaxation for biopolymers. In: Journal of Computational Biology. 1998 ; Vol. 5, No. 4. pp. 655-665.
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