Current Computer - Aided Drug Design - Volume 7, Issue 2, 2011

Understanding how drugs cause the desired effect on the organism is of utmost importance for drug design. This is not only a scientific motto, but also an economic issue which pharmaceutical companies have comprehended quite well. Understanding the relationship between the structure of a substance and its biological activity is critical for drug discovery. A wealth of knowledge has been generated to grasp such relationship Read More

Since the last half of the nineteenth century, molecular graphs have been present in several branches of chemistry. When used for molecular structure representation, they have been compared after mapping the corresponding graphs into mathematical objects. However, direct molecular comparison of molecular graphs is a research field less explored. The goal of this mini-review is to show some distance and similarity co Read More

We have shown in several papers the importance of using topology, particularly set-point topology, to deal with chemical questions related to the concept of similarity. The procedure developed has been called “chemotopology” and it has been applied to different chemical sets e.g. chemical elements, benzimidazoles, sterorids, amino acids and hydrides. The idea behind chemotopology is to run a hierarchical cluster analysis s Read More

Calculated atom pairs (APs) and a set of 369 topological indices (TIs) calculated by POLLY, Triplet, and Molconn-Z software were used to develop QSARs for anticancer activity of a group of 2-phenyl indoles. The TIs included both topostructural (TS) and topochemical (TC) indices. Results show that ridge regression using TS indices, TC indices, and atom pairs produced high-quality models for the prediction of anticancer activity Read More

Fifteen quantitative structure-activity relationship (QSAR) models developed by various authors for the prediction of mutagenicity of aromatic and heteroaromatic amines were analyzed and thirteen of them, based on 95 amines, were compared using their respective statistics and order theory (Hasse Diagram Technique, HDT) to obtain an ordering of QSAR models. The technique of Formal Concept Analysis (FCA) was applied to Read More

Drugs are devised to enter into the metabolism of an organism in order to produce a desired effect. From the chemical point of view, cellular metabolism is constituted by a complex network of reactions transforming metabolites one in each other. Knowledge on the structure of this network could help to develop novel methods for drug design, and to comprehend the root of known unexpected side effects. Many larg Read More

There are at least two significant applications of partial order theory in chemistry: Ranking methods and substances' properties prediction. In both cases, a set of objects is endowed with a partial order relation e.g. “more polluting than”, “can be obtained from”, “more reactive than” etc. The couple of set and partial order relation is known in mathematics as a partially ordered set (poset). Ranking methods, such as the Hasse Read More

Molecular docking has become an increasingly important tool for drug discovery. In this review, we present a brief introduction of the available molecular docking methods, and their development and applications in drug discovery. The relevant basic theories, including sampling algorithms and scoring functions, are summarized. The differences in and performance of available docking software are also discussed. Flexible re Read More