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 plays a major role in biomolecular recognition. In many cases, it is not
obvious how molecular structure will change upon association with other molecules. In …

Abstract Background Protein-protein interactions (PPIs) mediate the vast majority of
biological processes, therefore, significant efforts have been directed to investigate PPIs to …

Background A good scoring function is essential for molecular docking computations. In
conventional scoring functions, energy terms modeling pairwise interactions are …

Knowing the ligand or peptide binding site in proteins is highly important to guide drug
discovery, but experimental elucidation of the binding site is difficult. Therefore, various …

We present a series of molecular‐mechanics‐based protein refinement methods, including
two novel ones, applied as part of an induced fit docking procedure. The methods used …

This paper describes a new semi-flexible docking approach named Fado (flexible alignment
and docking), which incorporates flexibility by using an ensemble of precomputed ligand …

The aim of de novo protein design is to find the amino acid sequences that will fold into a
desired 3-dimensional structure with improvements in specific properties, such as binding …

The last few years have seen the development of numerous deep learning-based protein–
ligand docking methods. They offer huge promise in terms of speed and accuracy. However …

The importance of binding site plasticity in protein–ligand interactions is well-recognized,
and so are the difficulties in predicting the nature and the degree of this plasticity by …