A systematic study of low-resolution recognition in protein--protein complexes.
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 A(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.
Vakser
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Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA. vakseri@musc.edu
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Lam
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D000465:Algorithms; D001665:Binding Sites; D003460:Crystallization; D019992:Databases as Topic; D005583:Fourier Analysis; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D011956:Receptors, Cell Surface / Q000737:chemistry
D008024:Ligands; D011506:Proteins; D011956:Receptors, Cell Surface