The recognition process between a protein and a partner represents a significant theoretical
challenge. In silico structure-based drug design carried out with nothing more than the three …

Allostery describes altered protein function at one site due to a perturbation at another site.
One mechanism of allostery involves correlated motions, which can occur even in the …

Understanding protein interactions has broad implications for the mechanism of recognition,
protein design, and assigning putative functions to uncharacterized proteins. Studying …

We present a thermodynamical approach to identify changes in macromolecular structure
and dynamics in response to perturbations such as mutations or ligand binding, using an …

The shape of the protein surface dictates what interactions are possible with other
macromolecules, but defining discrete pockets or possible interaction sites remains difficult …

A new monotonicity-constrained maximum likelihood approach, called Partial Order
Optimum Likelihood (POOL), is presented and applied to the problem of functional site …

Staphylococcus aureus (S. aureus) causes many infections with significant morbidity and
mortality. S. aureus can form biofilms, which can cause biofilm-associated diseases and …

A new approach to predicting the ligand‐binding sites of proteins was developed, using
protein‐ligand docking computation. In this method, many compounds in a random library …

Backgrounds It is increasingly recognized that protein functions often require intricate
conformational dynamics, which involves a network of key amino acid residues that couple …

Background We propose a method for automatic extraction of protein-specific residue
mentions from the biomedical literature. The method searches text for mentions of amino …