Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor.

ABSTRACT: D3R 2016 Grand Challenge 2 focused on predictions of binding modes and affinities for 102 compounds against the farnesoid X receptor (FXR). In this challenge, two distinct methods, a docking-based method and a template-based method, were employed by our team for the binding mode prediction. For the new template-based method, 3D ligand similarities were calculated for each query compound against the ligands in the co-crystal structures of FXR available in Protein Data Bank. The binding mode was predicted based on the co-crystal protein structure containing the ligand with the best ligand similarity score against the query compound. For the FXR dataset, the template-based method achieved a better performance than the docking-based method on the binding mode prediction. For the binding affini

SUBMITTER: Duan R 

PROVIDER: S-EPMC5767536 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature