Esther Kellenberger

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A novel method to measure distances between druggable protein cavities is presented. Starting from user-defined ligand binding sites, eight topological and physicochemical properties are projected from cavity-lining protein residues to an 80 triangle-discretised sphere placed at the centre of the binding site, thus defining a cavity fingerprint.(More)
The sc-PDB is a collection of 6 415 three-dimensional structures of binding sites found in the Protein Data Bank (PDB). Binding sites were extracted from all high-resolution crystal structures in which a complex between a protein cavity and a small-molecular-weight ligand could be identified. Importantly, ligands are considered from a pharmacological and(More)
BACKGROUND The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein-ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the(More)
Quantification of local similarity between protein 3D structures is a promising tool in computer-aided drug design and prediction of biological function. Over the last ten years, several computational methods were proposed, mostly based on geometrical comparisons. This review summarizes the recent literature and gives an overview of available programs. A(More)
Structure-based virtual screening is a promising tool to identify putative targets for a specific ligand. Instead of docking multiple ligands into a single protein cavity, a single ligand is docked in a collection of binding sites. In inverse screening, hits are in fact targets which have been prioritized within the pool of best ranked proteins. The target(More)
Estimating the pairwise similarity of protein-ligand binding sites is a fast and efficient way of predicting cross-reactivity and putative side effects of drug candidates. Among the many tools available, three-dimensional (3D) alignment-dependent methods are usually slow and based on simplified representations of binding site atoms or surfaces. On the other(More)
Selectivity is a key factor in drug development. In this paper, we questioned the Protein Data Bank to better understand the reasons for the promiscuity of bioactive compounds. We assembled a data set of >1000 pairs of three-dimensional structures of complexes between a "drug-like" ligand (as its physicochemical properties overlap that of approved drugs)(More)
The sc-PDB database (available at is a comprehensive and up-to-date selection of ligandable binding sites of the Protein Data Bank. Sites are defined from complexes between a protein and a pharmacological ligand. The database provides the all-atom description of the protein, its ligand, their binding site and their(More)
The surface of thin sections of aldehyde-fixed biological material shows a specimen-related relief of 2-6 nm with Lowicryl. Epon sections are about three times smoother. The relief is the consequence of thin-sectioning being in reality a cleavage. Epitopes are supposed to be laid open (or set free) because cleavage follows the interfaces between protein and(More)
In electron micrographs of conventionally prepared thin sections of Escherichia coli one observes (i) a wavy appearance of the two membranes showing frequent appositions (named adhesion sites) and (ii) intermembrane bridges after plasmolysis which, it is claimed, occur at the adhesion sites and are related to intermembrane protein transport(More)