Título
A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations
Autor
David Israel Flores Granados
Colaborador
ROGERIO RAFAEL SOTELO MUNDO (Colaborador)
Brizuela Rodríguez, C. A. (Colaborador)
Nivel de Acceso
Acceso Abierto
Identificador alterno
doi: https://doi.org/10.1371/journal.pone.0108513
Materias
1UU9 protein, 3HRC protein, protein, thymidylate synthase, unclassified drug, protein kinase, thymidylate synthase, accuracy, algorithm, Article, CMASA, CMASA Substitution Matrix, Contact Matrix Average Deviation, controlled study, correlation coeffi - (SCOPUS) CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA - (CTI) MATEMÁTICAS - (CTI) ANÁLISIS NUMÉRICO - (CTI) ANÁLISIS NUMÉRICO - (CTI)
Resumen o descripción
The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file. © 2014 Flores et al.
Editor
Manuela Helmer-Citterich, University of Rome Tor Vergata, Italy
Fecha de publicación
2014
Tipo de publicación
Artículo
Versión de la publicación
Versión publicada
Recurso de información
Formato
application/pdf
Fuente
PLoS ONE, Vol.9, No.9, Pags.
Idioma
Inglés
Sugerencia de citación
Flores DI, Sotelo-Mundo RR, Brizuela CA (2014) A Simple Extension to the CMASA Method for the Prediction of Catalytic Residues in the Presence of Single Point Mutations. PLoS ONE 9(9): e108513. https://doi.org/10.1371/journal.pone.0108513
Repositorio Orígen
Repositorio Institucional CICESE
Descargas
23