Current Computer - Aided Drug Design - Volume 2, Issue 3, 2006

The increasing availability of atomic-level protein structures derived from X-ray crystallography and NMR spectroscopy, together with advances in computational power, have ushered in a new era of powerful theoretical approaches to study protein mechanisms and, by extension, use a computer-aided structural approach to drug design. Classical molecular dynamics calculations, in which Newton's equations of motion ar Read More

G-protein coupled receptors (GPCRs) are the largest single family of signaling molecules in mammals and represent approximately 2-3% of all genes in the human genome. Estimates of the total number of GPCR genes in the human genome range from about 750 to 1000. GPCRs mediate signaling by a wide variety of ligands including amino acids, ions, biogenic amines, peptides, glycoproteins, light, pheromones, and odor Read More

The dimensional expansion in the research domain of Selective Estrogen Receptor (ER) Modulators (SERM) has been driven by discovering molecules with improved endocrine profiles that might be safer and valuable drug candidates for treating variety of estrogen-linked pathologies. Desirable tissue selectivity may result from the unique structural characteristics of a ligand that take advantage of differences in diversit Read More

In recent years chemometrics has been undergoing an exciting development both in the applied areas and in the theoretical and methodological aspects. This review is focused on recent advances in chemometric methodologies for quantitative structure-activity relationship (QSAR) studies, and it covers multiple applications. QSAR is one of the tools for the computer-aided drug design; it is also an important branch of chemo Read More

With the advent of the post-genomic era, systems biology has set the stage for a quantum leap in our understanding of the fundamental cellular processes, phenotypic variations, and disease mechanisms. By integrating the vast amount data from genomics, transcriptomics, and proteomics analyses, systems biology seeks a holistic view of organisms and the modules that compose them. The approaches to a systems level vi Read More

The primary sequence of DNA is a sequence of nucleotides over the four-letters alphabet {A, C, G, T}. Characteristic sequences of a DNA sequence are given in term of classification of bases of nucleotides. Using the characteristic sequences, we construct a set of 3 x 8 matrices and a set of 2 x 2 matrices to represent DNA primary sequences and define the information entropy, which is based on counting all triplets of characteri Read More

Recently, the combination of state-of-the-art molecular mechanical force fields with continuum solvation models enables us to make relatively accurate predictions of both structures and free energies for macromolecules from molecular dynamics trajectories. The first part of this review is focused on the history and basic theory of free energy calculations based on physically effective energy functions. The second part illust Read More

We present a comprehensive but not exhaustive review of new trends in drug discovery and targets for cancer and AIDS which begins by highlighting the different historical stages of drug discovery from clinical diagnosis, natural compounds, serendipity and chemotherapy to the present age of modern experimental and computational techniques. The current state of the art of computer-aided drug design and sel Read More