Integrating Structure‐ and Ligand‐Based Virtual Screening: Comparison of Individual, Parallel, and Fused Molecular Docking and Similarity Search Calculations on Multiple Targets
Citations Over TimeTop 10% of 2008 papers
Abstract
Similarity searching is often used to preselect compounds for docking, thereby decreasing the size of screening databases. However, integrated structure- and ligand-based screening schemes are rare at present. Docking and similarity search calculations using 2D fingerprints were carried out in a comparative manner on nine target enzymes, for which significant numbers of diverse inhibitors could be obtained. In the absence of knowledge-based docking constraints and target-directed parameter optimisation, fingerprint searching displayed a clear preference over docking calculations. Alternative combinations of docking and similarity search results were investigated and found to further increase compound recall of individual methods in a number of instances. When the results of similarity searching and docking were combined, parallel selection of candidate compounds from individual rankings was generally superior to rank fusion. We suggest that complementary results from docking and similarity searching can be captured by integrated compound selection schemes.
Related Papers
- → CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein–ligand docking(2022)14 cited
- → Application of Conformational Clustering in Protein–Ligand Docking(2011)8 cited
- → Protein–Ligand Docking in Drug Design(2001)8 cited
- → Prediction of Protein-compound Complex Structures by Docking Simulation(2011)
- Study on similarity grade of immovable riverbed hydraulic model(2002)