Protein structure prediction using Rosetta in CASP12.
Proteins
; 86 Suppl 1: 113-121, 2018 03.
Article
en En
| MEDLINE
| ID: mdl-28940798
ABSTRACT
We describe several notable aspects of our structure predictions using Rosetta in CASP12 in the free modeling (FM) and refinement (TR) categories. First, we had previously generated (and published) models for most large protein families lacking experimentally determined structures using Rosetta guided by co-evolution based contact predictions, and for several targets these models proved better starting points for comparative modeling than any known crystal structure-our model database thus starts to fulfill one of the goals of the original protein structure initiative. Second, while our "human" group simply submitted ROBETTA models for most targets, for six targets expert intervention improved predictions considerably; the largest improvement was for T0886 where we correctly parsed two discontinuous domains guided by predicted contact maps to accurately identify a structural homolog of the same fold. Third, Rosetta all atom refinement followed by MD simulations led to consistent but small improvements when starting models were close to the native structure, and larger but less consistent improvements when starting models were further away.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Conformación Proteica
/
Proteínas
/
Modelos Moleculares
/
Pliegue de Proteína
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Biología Computacional
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Límite:
Humans
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
2018
Tipo del documento:
Article