HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids.
Bioinformatics
; 28(3): 342-9, 2012 Feb 01.
Article
em En
| MEDLINE
| ID: mdl-22171332
ABSTRACT
MOTIVATION Protein-protein interfaces contain important information about molecular recognition. The discovery of conserved patterns is essential for understanding how substrates and inhibitors are bound and for predicting molecular binding. When an inhibitor binds to different enzymes (e.g. dissimilar sequences, structures or mechanisms what we call cross-inhibition), identification of invariants is a difficult task for which traditional methods may fail. RESULTS:
To clarify how cross-inhibition happens, we model the problem, propose and evaluate a methodology called HydroPaCe to detect conserved patterns. Interfaces are modeled as graphs of atomic apolar interactions and hydrophobic patches are computed and summarized by centroids (HP-centroids), and their conservation is detected. Despite sequence and structure dissimilarity, our method achieves an appropriate level of abstraction to obtain invariant properties in cross-inhibition. We show examples in which HP-centroids successfully predicted enzymes that could be inhibited by the studied inhibitors according to BRENDA database.AVAILABILITY:
www.dcc.ufmg.br/~raquelcm/hydropace CONTACT valdetemg@ufmg.br; raquelcm@dcc.ufmg.br; santoro@icb.ufmg.br SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
Serina Proteases
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Limite:
Animals
Idioma:
En
Ano de publicação:
2012
Tipo de documento:
Article