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A Systematic Study of Low-Resolution Recognition in Protein-Protein Complexes
Ilya A. Vakser, Omar G. Matar and Chan F. Lam
Proceedings of the National Academy of Sciences of the United States of America
Vol. 96, No. 15 (Jul. 20, 1999), pp. 8477-8482
Published by: National Academy of Sciences
Stable URL: http://www.jstor.org/stable/48511
Page Count: 6
You can always find the topics here!Topics: Binding sites, Ligands, Databases, Receptors, Atoms, Energy, Molecules, Arithmetic mean, Center of mass, Biophysics
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A comprehensive nonredundant database of 475 cocrystallized protein-protein complexes was used to study low-resolution recognition, which was reported in earlier docking experiments with a small number of proteins. The docking program GRAMM was used to delete the atom-size structural details and systematically dock the resulting molecular images. The results reveal the existence of the low-resolution recognition in 52% of all complexes in the database and in 76% of the 113 complexes with an interface area >4,000 angstrom 2. Limitations of the docking and analysis tools used in this study suggest that the actual number of complexes with the low-resolution recognition is higher. However, the results already prove the existence of the low-resolution recognition on a broad scale.
Proceedings of the National Academy of Sciences of the United States of America © 1999 National Academy of Sciences