As structural genomics (SG) projects continue to deposit representative 3D structures of
proteins, homology modeling methods will play an increasing role in structure-based drug …

Major goal of structural biology involve formation of protein-ligand complexes; in which the
protein molecules act energetically in the course of binding. Therefore, perceptive of protein …

Consensus-scoring methods are commonly used with molecular docking in virtual screening
campaigns to filter potential ligands for a protein target. Traditional consensus methods …

Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales
are critical for understanding macromolecular functioning. Coarse-grained representations …

The interactions among associating (macro) molecules are dynamic, which adds to the
complexity of molecular recognition. While ligand flexibility is well accounted for in …

Ligand-docking-based methods are starting to play a critical role in lead discovery and
optimization, thus resulting in new 'drug-candidates'. They offer the possibility to go beyond …

Introduction: Protein–ligand interactions play key roles in various metabolic pathways, and
the proteins involved in these interactions represent major targets for drug discovery …

Here, we employed the collective motions extracted from Normal Mode Analysis (NMA) in
internal coordinates (torsional space) for the flexible fitting of atomic-resolution structures …

Here is presented an investigation of the use of normal modes in protein-protein docking,
both in theory and in practice. Upper limits of the ability of normal modes to capture the …

Background: Although virtual screening is now widely applied as a hit-finding methodology
within drug discovery programmes, there are relatively few reports of its contributing to …