Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential

• DOI: 10.1093/bioinformatics/btp449
• Publication Date: 2009-07-24T00:55:41Z
• Authors: Ami Levy-Moonshine; El-ad David Amir; Chen Keasar
• Keywords: Beta sheet; BETA (programming language)

Abstract Motivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches spend much time struggling escape numerous traps. Specifically, beta-sheet formation prone stray, many possible combinations hydrogen bonds are dead ends in terms assembly. It has been shown that cooperative for backbone ease this problem by augmenting bond patterns consistent with beta sheets. Here, we present novel hydrogen-bond term both effective promoting sheets and computationally efficient. In addition, the new differentiable operates on all-atom models. Results: Energy optimization poly-alanine chains under led significantly more content than non-cooperative term. Furthermore, optimized included very few non-native patterns. Availability: implemented within MESHI package freely available at http://cs.bgu.ac.il/∼meshi. Contact: [e-mail] Supplementary information: data Bioinformatics online.