Mapping of ligand-binding cavities in proteins.

ABSTRACT: The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterize and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity, and charge). This approach can provide valuable information on the similarities and dissimilarities, of binding cavities due to mutations, between-species differences and flexibility upon ligand-binding. The presented results show that information on ligand-binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predict

SUBMITTER: Andersson CD 

PROVIDER: S-EPMC2957484 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature