Closing the side-chain gap in protein loop modeling.
J Comput Aided Mol Des
; 23(7): 411-8, 2009 Jul.
Article
em En
| MEDLINE
| ID: mdl-19459054
ABSTRACT
The success of structure-based drug design relies on accurate protein modeling where one of the key issues is the modeling and refinement of loops. This study takes a critical look at modeled loops, determining the effect of re-sampling side-chains after the loop conformation has been generated. The results are evaluated in terms of backbone and side-chain conformations with respect to the native loop. While models can contain loops with high quality backbone conformations, the side-chain orientations could be poor, and therefore unsuitable for ligand docking and structure-based design. In this study, we report on the ability to model loop side-chains accurately using a variety of commercially available algorithms that include rotamer libraries, systematic torsion scans and knowledge-based methods.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Proteínas
/
Homologia Estrutural de Proteína
Idioma:
En
Revista:
J Comput Aided Mol Des
Ano de publicação:
2009
Tipo de documento:
Article