ClusPro LigTBM: Automated Template-based Small Molecule Docking.

ABSTRACT: The template-based approach has been essential for achieving high-quality models in the recent rounds of blind protein-protein docking competition CAPRI (Critical Assessment of Predicted Interactions). However, few such automated methods exist for protein-small molecule docking. In this paper, we present an algorithm for template-based docking of small molecules. It searches for known complexes with ligands that have partial coverage of the target ligand, performs conformational sampling and template-guided energy refinement to produce a variety of possible poses, and then scores the refined poses. The algorithm is available as the automated ClusPro LigTBM server. It allows the user to specify the target protein as a PDB file and the ligand as a SMILES string. The server then searches for

SUBMITTER: Alekseenko A 

PROVIDER: S-EPMC7890944 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature