AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters.

ABSTRACT: Modern rational modulator design and structure-function characterization often concentrate on concave regions of biomolecular surfaces, ranging from well-defined small-molecule binding sites to large protein-protein interaction interfaces. Here, we introduce a β-cluster as a pseudomolecular representation of fragment-centric pockets detected by AlphaSpace [J. Chem. Inf. Model. 2015, 55, 1585], a recently developed computational analysis tool for topographical mapping of biomolecular concavities. By mimicking the shape as well as atomic details of potential molecular binders, this new β-cluster representation allows direct pocket-to-ligand shape comparison and can be used to guide ligand optimization. Furthermore, we defined the β-score, the optimal Vina score of the β-

SUBMITTER: Katigbak J 

PROVIDER: S-EPMC7093224 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature