Using tetrahedral grid-based protein models in docking

Protein-protein recognition, leading to the formation of specific functional complexes, involves complementary surfaces of interacting subunits. Current docking protocols employ complex scoring functions, neglecting proper shape matching by the use of cubic grids. In the present paper a docking algo...

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Bibliographic Details
Published in:Journal of physics. Condensed matter 2007-07, Vol.19 (28), p.285209-285209 (8)
Main Authors: Wieczorek, G, Zielenkiewicz, P
Format: Article
Language:English
Subjects:
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
Miscellaneous
Molecular biophysics
Physico-chemical properties of biomolecules
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Summary:Protein-protein recognition, leading to the formation of specific functional complexes, involves complementary surfaces of interacting subunits. Current docking protocols employ complex scoring functions, neglecting proper shape matching by the use of cubic grids. In the present paper a docking algorithm based on the tetrahedral grid model of proteins is described, allowing a more precise description of shape complementarity. The software was tested on the docking benchmark, giving excellent results for rigid-body docking. Extension of the present methodology to flexible docking is in progress.
ISSN:0953-8984
1361-648X
DOI:10.1088/0953-8984/19/28/285209