Molecular Docking Simulation

On the Difficulty to Rescore Hits from Ultralarge Docking Screens.

Docking-based virtual screening tools customized to mine ultralarge chemical spaces are consistently reported to yield both higher hit rates and more potent ligands than that …

Sindt, F.

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein.

The CACHE challenges are a series of prospective benchmarking exercises to evaluate progress in the field of computational hit-finding.

Li, F.

Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2.

We herewith applied a priori a generic hit identification method (POEM) for difficult targets of known three-dimensional structure, relying on the simple knowledge of …

Eguida, M.

True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better.

Hundreds of fast scoring functions have been developed over the last 20 years to predict binding free energies from three-dimensional structures of protein-ligand complexes.

Tran-Nguyen, V.

A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design.

Identifying local similarities in binding sites from distant proteins is a major hurdle to rational drug design.

Eguida, M.

All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening

Discovering the very first ligands of pharmacologically important targets in a fast and cost-efficient manner is an important issue in drug discovery.

Tran-Nguyen, V.