Current Pharmaceutical Design - Volume 13, Issue 14, 2007

In recent years, biomedical research and drug design became one of the fastest growing branches of scientific and industrial development. The tremendous scale (number of projects and volume of information to process) promoted by trillions of dollars invested in these fields called for completely new approaches to obtain, analyze, and apply information to clinical practice, pharmacological research and the medical ind Read More

Accurately identifying functional sites in proteins is one of the most important topics in bioinformatics and systems biology. In bioinformatics, identifying protease cleavage sites in protein sequences can aid drug/inhibitor design. In systems biology, post-translational protein-protein interaction activity is one of the major components for analyzing signaling pathway activities. Determining functional sites using laborato Read More

To understand most cellular processes, one must understand how genetic information is processed. A formidable challenge is the dissection of gene regulatory networks to delineate how eukaryotic cells coordinate and govern patterns of gene expression that ultimately lead to a phenotype. In this paper, we review several approaches for modeling eukaryotic gene regulatory networks and for reverse engineering such networks Read More

Synaptic transmission requires that the binding of the transmitter to the receptor to occur under rapidly changing transmitter levels, and this binding interaction is unlikely to be at equilibrium. We have sought to numerically solve for binding kinetics using ordinary differential equations and simultaneous difference equations for use in stochastic conditions. The reaction scheme of GABA interacting with the ligand-gated ion-c Read More

At present, computer-assisted molecular modeling and virtual screening have become effective and widelyused tools for drug design. However, a prerequisite for design and synthesis of a therapeutic agent is determination of a correct target in the metabolic system, which should be either inhibited or stimulated. Solution of this extremely complicated problem can also be assisted by computational methods. This review disc Read More

The aim of this paper is to introduce the reader to new developments in Neural Networks and Kernel Machines concerning the treatment of structured domains. Specifically, we discuss the research on these relatively new models to introduce a novel and more general approach to QSPR/QSAR analysis. The focus is on the computational side and not on the experimental one.

Pattern recognition, machine learning and artificial intelligence approaches play an increasingly important role in rational drug design, screening and identification of candidate molecules and studies on quantitative structure-activity relationships (QSAR). In this review, we present an overview of basic concepts and methodology in the fields of machine learning and artificial intelligence (AI). An emphasis is put on methods that e Read More