IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.
Bioinformatics
; 33(12): 1806-1813, 2017 Jun 15.
Article
en En
| MEDLINE
| ID: mdl-28200016
ABSTRACT
MOTIVATION In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. RESULTS:
Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. AVAILABILITY AND IMPLEMENTATION IRaPPA has been implemented in the SwarmDock server ( http//bmm.crick.ac.uk/â¼SwarmDock/ ), pyDock server ( http//life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http//zdock.umassmed.edu/ ), with code available on request. CONTACT moal@ebi.ac.uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Conformación Proteica
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Programas Informáticos
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Almacenamiento y Recuperación de la Información
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Mapeo de Interacción de Proteínas
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Simulación del Acoplamiento Molecular
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2017
Tipo del documento:
Article
País de afiliación:
Reino Unido
Pais de publicación:
ENGLAND
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ESCOCIA
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GB
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GREAT BRITAIN
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INGLATERRA
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REINO UNIDO
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SCOTLAND
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UK
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UNITED KINGDOM