Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential.
Bioinformatics
; 25(20): 2639-45, 2009 Oct 15.
Article
en En
| MEDLINE
| ID: mdl-19628506
ABSTRACT
MOTIVATION The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models. RESULTS:
Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns.AVAILABILITY:
The new term is implemented within the MESHI package and is freely available at http//cs.bgu.ac.il/ approximately meshi.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Proteínas
/
Estructura Secundaria de Proteína
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2009
Tipo del documento:
Article
País de afiliación:
Israel