Here we present version 2.0 of HADDOCK, which incorporates considerable improvements
and new features. HADDOCK is now able to model not only protein–protein complexes but …

Abstract The CAPRI experiment (Critical Assessment of Predicted Interactions) simulates
realistic and diverse docking challenges, each case having specific properties that may be …

The prediction of protein–protein complexes from the structures of unbound components is a
challenging and powerful strategy to decipher the mechanism of many essential biological …

Highlights•The best servers based on “free” docking methods find acceptable models
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …

Protein–protein docking is an important computational tool for predicting protein–protein
interactions. With the rapid development of proteomics projects, more and more …

We have shown previously that given high-resolution structures of the unbound molecules,
structure determination of protein complexes is possible by including biochemical and/or …

Here, we present FireDock, an efficient method for the refinement and rescoring of rigid‐
body docking solutions. The refinement process consists of two main steps:(1) …

Reliability in docking of ligand molecules to proteins or other targets is an important
challenge for molecular modeling. Applications of the docking technique include not only …

Background Macromolecular complexes are the molecular machines of the cell. Knowledge
at the atomic level is essential to understand and influence their function. However, their …

Abstract Characterization of life processes at the molecular level requires structural details of
protein interactions. The number of experimentally determined structures of protein–protein …