Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories

Klara Kedem, L. Paul Chew, Ron Elber

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


The Unit-vector RMS (URMS) is a new technique to compare protein chains and to detect similarities of chain segments. It is limited to comparison of C(α) chains. However, it has a number of unique features that include exceptionally weak dependence on the length of the chain and efficient detection of substructure similarities. Two molecular dynamics simulations of proteins in the neighborhood of their native states are used to test the performance of the URMS. The first simulation is of a solvated myoglobin and the second is of the protein MHC. In accord with previous studies the secondary structure elements (helices or sheets) are found to be moving relatively rigidly among flexible loops. In addition to these tests, folding trajectories of C peptides are analyzed, revealing a folding nucleus of seven amino acids.

Original languageEnglish
Pages (from-to)554-564
Number of pages11
JournalProteins: Structure, Function and Bioinformatics
Issue number4
StatePublished - 1 Dec 1999
Externally publishedYes


  • C peptide
  • Folding
  • Order parameter
  • Root mean square distance
  • Structure comparison

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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