Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

FTMap is a computational mapping server that identifies binding hot spots of
macromolecules—ie, regions of the surface with major contributions to the ligand-binding …

The exploration of privileged structures in drug discovery is a rapidly emerging theme in
medicinal chemistry. These structures represent a class of molecules capable of binding to …

A nuclear magnetic resonance (NMR)-based method is described in which small organic
molecules that bind to proximal subsites of a protein are identified, optimized, and linked …

Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …

Motivation: The binding sites of proteins generally contain smaller regions that provide major
contributions to the binding free energy and hence are the prime targets in drug design …

An analysis of heteronuclear-NMR-based screening data is used to derive relationships
between the ability of small molecules to bind to a protein and various parameters that …

Molecular docking is the methodology of choice for studying in silico protein-ligand binding
and for prioritizing compounds to discover new lead candidates. Traditional docking …

Molecular docking remains an important tool for structure-based screening to find new
ligands and chemical probes. As docking ambitions grow to include new scoring function …