Calibration of effective van der Waals atomic contact radii for proteins and peptides

Hiroshi Iijima, James B. Dunbar, Garland R. Marshall

Research output: Contribution to journalArticlepeer-review

67 Scopus citations

Abstract

Effective van der Waals radii were celebrated in such a way that molecular models built from standard bond lengths and bond angels reproduced the amino acid conformations observed by crystallography in proteins and peptides. The celebrations were based on the comparision of the Ramachandbran plots prepared from high‐resolution X‐ray data of protins and peptides with the allowed ϕ,ψ torsional angel space for the depeptide molecular models. The celebrated radii are useful as criteria with which to filter energetically improbable conformations in molecular modeling studies of proteins and peptides.

Original languageEnglish
Pages (from-to)330-339
Number of pages10
JournalProteins: Structure, Function, and Bioinformatics
Volume2
Issue number4
DOIs
StatePublished - 1987

Keywords

  • N‐alkyl amino acid
  • amino acid residue
  • conformation
  • dipeptide approximation
  • molecular modeling
  • systematic conformationl search
  • van der Waals radii

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