Title:	SUPPORTING INTERMOLECULAR INTERACTION ANALYSES OF FLEXIBLE-RECEPTOR DOCKING SIMULATIONS
Author(s):	Ana T. Winck, Karina S. Machado, Osmar Norberto de Souza, Duncan D. Ruiz
ISBN:	978-972-8939-30-4
Editors:	Hans Weghorn, Pedro Isaías and Radu Vasiu
Year:	2010
Edition:	Single
Keywords:	Data Repository, Drug Design, Flexible Receptor, Molecular Docking
Type:	Full Paper
First Page:	183
Last Page:	190
Language:	English
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Paper Abstract:	Nowadays, with the growth of biological experiments, solving and analyzing the massive amount of data being generated has been one of the challenges in bioinformatics. One important research area in bioinformatics is the rational drug design (RDD), centered on examining possible interactions between receptors and ligands, usually performed by molecular docking. Very little is known about the effectiveness of considering the flexibility of a receptor molecule in current molecular docking simulations when this flexibility is modeled by a molecular dynamics (MD) simulation. This methodology generates vast amounts of data which need to be explored in order to generate useful information about receptor-ligand interactions. To better interpret these data we developed a comprehensive repository that integrates features of all snapshots from a MD simulation trajectory with related data about receptor-ligand interactions from the docking simulations results. The prepared and stored data allowed the identification of residues that interact often with the tested ligands and that would not be seen in docking simulations with a rigid structure. We ranked, for each ligand, the top 10 receptor residues that interact in most of the docking runs, totalizing in 25 distinct residues for our receptor. These information would be arduous to obtain without our repository, as well as it cannot be assessed using a rigid receptor conformation, showing the importance of the receptor flexibility in molecular docking simulations.
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