Identification of Ligand Binding Site and Protein-Protein Interaction Area [Paperback]

This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It should be noted that there are many other theoretical studies devoted to predicting the activity of specific proteins and that useful protein data can be found in numerous databases. The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. Developing such tools is not an easy task  it requires extensive expertise in the area of molecular biology as well as a firm grasp of numerical modeling methods. Thus, it is often viewed as a prime candidate for interdisciplinary research.

This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It offers a comparative analysis of models based on geometry versus those based on knowledge of the biological phenomenon.

Contributors.- Foreword.- Chapter 1 SuMo: a tool for protein function inference based on 3D structures comparisons, J-A. Chemelle, E. Bettler, CH. Combet, R. Terreux, CH. Geourjon, G. Deleage.- Chapter 2 Identification of pockets on protein surface to predict proteinligand binding sites, Binding Huang.- Chapter 3 Can the structure of the hydrophobic core determine the complexation site?, M. Banach, L. Konieczny, I. Roterman.- Chapter 4 Comparative analysis of techniques oriented on the recognition of ligand binding area in proteins, P. Alejster, M. Banach, W. Jurkowski, D. Marchewka, I. Roterman.- Chapter 5 Docking predictions of protein-protein interactions and their assessment: the CAPRI experiment, Joel Janin.- Chapter 6 Prediction of protein-protein binding interfaces, D. Marchewka, W. Jurkowski, M. Banach, I. Roterman.- Chapter 7 Support for Cooperative Experiments in e-Science: From Scientific Workflows to Knol#