Molecular Informatics utilises many ideas and concepts to find relationships between
molecules. The concept of similarity, where molecules may be grouped according to their …

Accelerating the drug discovery process requires predictive computational protocols
capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking …

Background Computational methods utilizing the structural and functional information help
to understand specific molecular recognition events between the target biomolecule and …

Ligand binding affinity prediction is one of the most important applications of computational
chemistry. However, accurately ranking compounds with respect to their estimated binding …

We report here a robust automated active site detection, docking, and scoring (AADS)
protocol for proteins with known structures. The active site finder identifies all cavities in a …

Dopamine neurotransmitter and its receptors play a critical role in the cell signaling process
responsible for information transfer in neurons functioning in the nervous system …

We demonstrate that using an all-atom molecular mechanics force field combined with an
implicit solvent model for scoring protein− ligand complexes is a promising approach for …

The presence of water molecules plays an important role in the accuracy of ligand− protein
docking predictions. Comprehensive docking simulations have been performed on a large …

Background The number of protein targets with a known or predicted tri-dimensional
structure and of drug-like chemical compounds is growing rapidly and so is the need for new …

Automated docking strategies successfully applied to binding mode predictions of ligands in
Cyt P450 crystal structures in an earlier study (de Graaf et al. J. Med. Chem. 2005, 7, 2308 …