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Curr Opin Struct Biol. 2009 Aug;19(4):458-63. doi: 10.1016/j.sbi.2009.07.005. Epub 2009 Jul 29.

Computational design of affinity and specificity at protein-protein interfaces.

Author information

1
Center for Bioinformatics and Department of Molecular Biosciences, 1200 Sunnyside Avenue, University of Kansas, Lawrence, KS 66045-7534, USA.

Abstract

The computer-based design of protein-protein interactions is a rigorous test of our understanding of molecular recognition and an attractive approach for creating novel tools for cell and molecular research. Considerable attention has been placed on redesigning the affinity and specificity of naturally occurring interactions. Several studies have shown that reducing the desolvation costs for binding while preserving shape complimentarity and hydrogen bonding is an effective strategy for improving binding affinities. In favorable cases specificity has been designed by focusing only on interactions with the target protein, while in cases with closely related off-target proteins it has been necessary to explicitly disfavor unwanted binding partners. The rational design of protein-protein interactions from scratch is still an unsolved problem, but recent developments in flexible backbone design and energy functions hold promise for the future.

PMID:
19646858
PMCID:
PMC2882636
DOI:
10.1016/j.sbi.2009.07.005
[Indexed for MEDLINE]
Free PMC Article

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