Binding Sites

Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways.

G protein-coupled receptors (GPCRs) constitute a functionally diverse protein family and are targets for a broad spectrum of pharmaceuticals.

Aranda-García, D.

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.

Estimating the Similarity between Protein Pockets.

With the exponential increase in publicly available protein structures, the comparison of protein binding sites naturally emerged as a scientific topic to explain observations or …

Eguida, M.

Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision.

Rationalizing the identification of hidden similarities across the repertoire of druggable protein cavities remains a major hurdle to a true proteome-wide structure-based …

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.

Structure-Based Detection of Orthosteric and Allosteric Pockets at Protein-Protein Interfaces

Protein-protein interfaces represent challenging but very promising targets to discover novel drugs with exquisite specificity profiles.

Da Silva, F.

A rationally designed oligopeptide shows significant conformational changes upon binding to sulphate ions.

Oligopeptides that interact with oxoanions were developed by rational design methods.

Demuth, C.

NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosphoenolpyruvate:sugar phosphotransferase enzyme I.

Starting from the NMR structure of the binary complex between the N-terminal domain of the unphosphorylated enzyme I (EIN) of the phosphoenolpyruvate:sugar phosphotransferase (PTS) …

Rognan, D.