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

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 -alpha chains. However, it has a number of unique features that include exc eptionally weak dependence on the length of the chain and efficient detecti on of substructure similarities. Two molecular dynamics simulations of prot eins in the neighborhood of their native states are used to test the perfor mance 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 r igidly among flexible loops, In addition to these tests, folding trajectori es of C peptides are analyzed, revealing a folding nucleus of seven amino a cids, Proteins 1999;37: 554-564, (C) 1999Wiley-Liss, Inc.