Structural information about protein‐protein interactions, often missing at the interactome
scale, is important for mechanistic understanding of cells and rational discovery of …

Protein–protein docking technology is an effective approach to study the molecular
mechanism of essential biological processes mediated by complex protein–protein …

We present a novel optimization approach to train a free-shape distance-dependent protein-
ligand scoring function called Convex-PL. We do not impose any functional form of the …

Motivation Docking prediction algorithms aim to find the native conformation of a complex of
proteins from knowledge of their unbound structures. They rely on a combination of …

Motivation The root mean square deviation (RMSD) is one of the most used similarity criteria
in structural biology and bioinformatics. Standard computation of the RMSD has a linear …

We report the performance of protein–protein docking predictions by our group for recent
rounds of the Critical Assessment of Prediction of Interactions (CAPRI), a community‐wide …

Abstract The 2015 D3R Grand Challenge provided an opportunity to test our new model for
the binding free energy of small molecules, as well as to assess our protocol to predict …

Motivation Protein–protein interactions are crucial in almost all biological processes.
Proteins interact through their interfaces. It is important to determine how proteins interact …

The 2013–2014 CSAR docking exercise was the opportunity to assess the performance of
the novel knowledge-based potential we are developing, named Convex-PL. The data used …

Conformational ensembles comprise one of the fundamental concepts in statistical
bioinformatics and appear in a variety of applications, eg molecular docking, virtual …