Conformational selection emerges as a theme in macromolecular interactions. Data validate
it as a prevailing mechanism in protein–protein, protein–DNA, protein–RNA, and protein …

Protein flexibility and induced fit effects present a major obstacle to the development of
better molecular docking algorithms and scoring functions. Here we present several …

Understanding the ruling principles whereby protein receptors recognize, interact, and
associate with molecular substrates and inhibitors is of paramount importance in drug …

We present a reliable and accurate solution to the induced fit docking problem for protein–
ligand binding by combining ligand-based pharmacophore docking, rigid receptor docking …

Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …

Accurate modeling of protein ligand binding is an important step in structure-based drug
design, is a useful starting point for finding new lead compounds or drug candidates. The …

Main goal in drug discovery is the identification of drug-like compounds capable to modulate
specific biological targets. Thus, the prediction of reliable binding poses of candidate …

Virtual high-throughput screening of molecular databases and in particular high-throughput
protein–ligand docking are both common methodologies that identify and enrich hits in the …

Abstract Knowledge of protein–ligand complexes is essential for efficient drug design.
Virtual docking can bring important information on putative complexes but it is still far from …

Introduction: The volume of three-dimensional structural information of macromolecules and
the number of computational tools to predict binding modes and affinities of molecular …