Template-based protein structure modeling using the RaptorX web server.
Nat Protoc
; 7(8): 1511-22, 2012 Jul 19.
Article
en En
| MEDLINE
| ID: mdl-22814390
ABSTRACT
A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http//raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Proteínas
/
Modelos Moleculares
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Nat Protoc
Año:
2012
Tipo del documento:
Article
País de afiliación:
Estados Unidos