Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …

The docking field has come of age. The time is ripe to present the principles of docking,
reviewing the current state of the field. Two reasons are largely responsible for the maturity …

Accurate and fast structure prediction of peptides of less 40 amino acids in aqueous solution
has many biological applications, but their conformations are pH-and salt concentration …

We describe a comparative protein modelling method designed to find the most probable
structure for a sequence given its alignment with related structures. The three dimensional …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

This article reviews machine learning methods for bioinformatics. It presents modelling
methods, such as supervised classification, clustering and probabilistic graphical models for …

All published rotamer libraries contain some rotamers that exhibit impossible internal atomic
overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues …

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) …

A backbone-dependent rotamer library for amino acid side-chains is developed and used for
constructing protein side-chain conformations from the main-chain co-ordinates. The …

Rotamer libraries are widely used in protein structure prediction, protein design, and
structure refinement. As the size of the structure data base has increased rapidly in recent …