Molecular docking is a process through which small molecules are docked into the
macromolecular structures for scoring its complementary values at the binding sites. It is a …

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 …

The development of scoring functions is of great importance to protein docking. Here we
present a new scoring function for the initial stage of unbound docking. It combines our …

The double cubic lattice method (DCLM) is an accurate and rapid approach for computing
numerically molecular surface areas (such as the solvent accessible or van der Waals …

Folding funnels have been the focus of considerable attention during the last few years.
These have mostly been discussed in the general context of the theory of protein folding …

Computer-based methods for predicting the structure of ligand–protein complexes or
docking algorithms have application in both drug design and the elucidation of biochemical …

Background: An important prerequisite for computa- potential new drug against AIDS, into
HIV-l protease. tional structure-based drug design is prediction of the For this molecule …

Whereas previously we have successfully utilized the folding funnels concept to rationalize
binding mechanisms (Ma B, Kumar S, Tsai CJ, Nussinov R, 1999, Protein Eng 12: 713–720) …

The assumption that crystal contacts reflect natural macromolecular interactions makes a
basis for many studies in structural biology. However, the crystal state may correspond to a …

A comprehensive docking study was performed on 27 distinct protein‐protein complexes.
For 13 test systems, docking was performed with the unbound X‐ray structures of both the …