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

• Published in: Proteins, structure, function, and bioinformatics Vol. 37; no. 4; pp. 554 - 564
• Main Authors: Kedem, Klara, Chew, L. Paul, Elber, Ron
• Format: Journal Article
• Language: English
• Published: New York John Wiley & Sons, Inc 01-12-1999
• Subjects: Algorithms; C peptide; folding; Histocompatibility Antigens - chemistry; Myoglobin - chemistry; order parameter; Protein Folding; Proteins - chemistry; root mean square distance; structure comparison; Thermodynamics
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/(SICI)1097-0134(19991201)37:4<554::AID-PROT6>3.0.CO;2-1

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 Cα 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. Proteins 1999;37:554–564. ©1999 Wiley‐Liss, Inc.