average and extreme multi-atom van der waals interactions strong coupling of multi-atom van der waals interactions with covalent bonding平均和极端multi-atom范德瓦耳斯相互作用强耦合与共价键multi-atom范德华相互作用.pdfVIP

Chemistry Central Journal Research article Open Access Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding Alexei V Finkelstein Address: Institute of Protein Research, Russian Academy of Sciences,142290, Pushchino, Moscow Region, Russia Email: Alexei V Finkelstein - afinkel@tres.ru Published: 30 July 2007 Received: 30 March 2007 Accepted: 30 July 2007 Chemistry Central Journal 2007, 1:21 doi:10.1186/1752-153X-1-21 This article is available from: /content/1/1/21 © 2007 Finkelstein et al This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 interact