Average and extreme multi-atom Van der Waals interactions: strong coupling of multi-atom Van der Waals interactions with covalent bonding.

ABSTRACT:

Background

The prediction of ligand binding or protein structure requires very accurate force field potentials - even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation.

Results

A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interactio

SUBMITTER: Finkelstein AV 

PROVIDER: S-EPMC1988792 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature