ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.
Proteins
; 88(8): 1082-1090, 2020 08.
Article
en En
| MEDLINE
| ID: mdl-32142178
ABSTRACT
Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template-based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template-based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use at https//tbm.cluspro.org, is demonstrated by predicting the protein-protein targets of rounds 38 to 45 of CAPRI.
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Péptidos
/
Programas Informáticos
/
Proteínas
/
Simulación del Acoplamiento Molecular
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
2020
Tipo del documento:
Article
País de afiliación:
Estados Unidos