Current Computer - Aided Drug Design - Volume 5, Issue 3, 2009

No biological process can be fully described by computational techniques unless water is taken into consideration. Unfortunately, accurate representation of the water environment in any biological process is normally too timeconsuming with present techniques. Commonly, in ligand-binding docking, all water molecules are removed from the experimental structure data before the system is prepared, in which case it i Read More

Activation of voltage-dependent K+ (Kv) channels modulates cellular excitability in several physiological systems including neuronal and cardiac cells. Given recent progress in structure determination and in computation technology, molecular dynamics (MD) simulation analyses have become a valuable tool in studies of voltage-dependent gating of Kv channels. However, due to the complex voltage-sensing mechanisms and int Read More

Reverse transcriptase (RT), an essential enzyme for HIV-1 (human immunodeficiency virus type-1) life cycle, is a key target in drug discovery efforts against HIV-1 infection. Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are very specific to HIV-1 RT and have relatively less toxicity than the nucleoside reverse transcriptase inhibitors (NRTIs). However, the rapid emergence of drug-resistant viral strains has limited the ther Read More

Quantitative structure-activity relationships (QSARs) techniques are routinely used in modern computer-aided drug design. In this review, the common generalization and computational procedures of QSAR methods (CoMFA, CoMSIA, and HQSA) are described in detail. The predictive ability of CoMFA and CoMSIA models depends directly on the quality of molecular alignment, the selection of probe, the difference of steps and Read More