Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14.
Proteins
; 89(12): 1722-1733, 2021 12.
Article
en En
| MEDLINE
| ID: mdl-34331359
ABSTRACT
The trRosetta structure prediction method employs deep learning to generate predicted residue-residue distance and orientation distributions from which 3D models are built. We sought to improve the method by incorporating as inputs (in addition to sequence information) both language model embeddings and template information weighted by sequence similarity to the target. We also developed a refinement pipeline that recombines models generated by template-free and template utilizing versions of trRosetta guided by the DeepAccNet accuracy predictor. Both benchmark tests and CASP results show that the new pipeline is a considerable improvement over the original trRosetta, and it is faster and requires less computing resources, completing the entire modeling process in a median < 3 h in CASP14. Our human group improved results with this pipeline primarily by identifying additional homologous sequences for input into the network. We also used the DeepAccNet accuracy predictor to guide Rosetta high-resolution refinement for submissions in the regular and refinement categories; although performance was quite good on a CASP relative scale, the overall improvements were rather modest in part due to missing inter-domain or inter-chain contacts.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Proteínas
/
Estructura Terciaria de Proteína
/
Biología Computacional
/
Aprendizaje Profundo
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Límite:
Humans
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
2021
Tipo del documento:
Article
País de afiliación:
Estados Unidos