3DLigandSite: structure-based prediction of protein-ligand binding sites.

ABSTRACT: 3DLigandSite is a web tool for the prediction of ligand-binding sites in proteins. Here, we report a significant update since the first release of 3DLigandSite in 2010. The overall methodology remains the same, with candidate binding sites in proteins inferred using known binding sites in related protein structures as templates. However, the initial structural modelling step now uses the newly available structures from the AlphaFold database or alternatively Phyre2 when AlphaFold structures are not available. Further, a sequence-based search using HHSearch has been introduced to identify template structures with bound ligands that are used to infer the ligand-binding residues in the query protein. Finally, we introduced a machine learning element as the final prediction step, which improve

SUBMITTER: McGreig JE 

PROVIDER: S-EPMC9252821 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature