Delaunay-based nonlocal interactions are sufficient and accurate in protein fold recognition.
Proteins
; 82(3): 415-23, 2014 Mar.
Article
en En
| MEDLINE
| ID: mdl-24038726
ABSTRACT
This study is aimed at showing that considering only nonlocal interactions (interactions of two atoms with a sequence separation larger than five amino acids) extracted using Delaunay tessellation is sufficient and accurate for protein fold recognition. An atomic knowledge-based potential was extracted based on a Delaunay tessellation with 167 atom types from a sample of the native structures and the normalized energy was calculated for only nonlocal interactions in each structure. The performance of this method was tested on several decoy sets and compared to a method considering all interactions extracted by Delaunay tessellation and three other popular scoring functions. Features such as the contents of different types of interactions and atoms with the highest number of interactions were also studied. The results suggest that considering only nonlocal interactions in a Delaunay tessellation of protein structure is a discrete structure catching deep properties of the three-dimensional protein data.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Conformación Proteica
/
Proteínas
/
Pliegue de Proteína
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
2014
Tipo del documento:
Article
País de afiliación:
Irán