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Proceedings Paper

Visualization tool for simulating ligand-receptor binding process
Author(s): Karl Geppert; Binh Pham; R. Quinn
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Paper Abstract

Ligand-receptor protein binding is an important process in drug design. This paper discusses the development of a visual tool for studying the binding of ligand-receptor pairs, to help in identifying active sites of the molecules. The tool can be used to explore many possible variations in binding pairs without doing expensive laboratory experiments. The traditional view of the binding process has been limited to a static lock and key model. It is now regarded that the ligand and receptor change dynamically during the interaction. Traditional experimental methods only determine the shape of static chemical structures. Our tool improves on the previous methods by dynamically simulating the entire binding process of isolated ligand-receptor pairs. The open design of our dynamic interaction model allows its extension with further constraints and heuristic rules. This is needed when the existing forces do not provide a sufficiently complete system description. For example, more detailed simulation constraints can increase the probability of convergence of a ligand-receptor pair. New constraints can limit the degree of freedom of rotation about bonds, to take into account molecular affinity. The intermolecular rules may be changed to include the effects of hydrogen bonding, and other forces.

Paper Details

Date Published: 8 March 1996
PDF: 6 pages
Proc. SPIE 2656, Visual Data Exploration and Analysis III, (8 March 1996); doi: 10.1117/12.234676
Show Author Affiliations
Karl Geppert, Griffith Univ. (Australia)
Binh Pham, Univ. of Ballarat (Australia)
R. Quinn, Griffith Univ. (Australia)


Published in SPIE Proceedings Vol. 2656:
Visual Data Exploration and Analysis III
Georges G. Grinstein; Robert F. Erbacher, Editor(s)

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