Document Detail

An accurate binding interaction model in de novo computational protein design of interactions: If you build it, they will bind.
MedLine Citation:
PMID:  23558036     Owner:  NLM     Status:  Publisher    
Computational protein design efforts aim to create novel proteins and functions in an automated manner and, in the process, these efforts shed light on the factors shaping natural proteins. The focus of these efforts has progressed from the interior of proteins to their surface and the design of functions, such as binding or catalysis. Here we examine progress in the development of robust methods for the computational design of non-natural interactions between proteins and molecular targets such as other proteins or small molecules. This problem is referred to as the de novo computational design of interactions. Recent successful efforts in de novo enzyme design and the de novo design of protein-protein interactions open a path towards solving this problem. We examine the common themes in these efforts, and review recent studies aimed at understanding the nature of successes and failures in the de novo computational design of interactions. While several approaches culminated in success, the use of a well-defined structural model for a specific binding interaction in particular has emerged as a key strategy for a successful design, and is therefore reviewed with special consideration.
Nir London; Xavier Ambroggio
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-4-1
Journal Detail:
Title:  Journal of structural biology     Volume:  -     ISSN:  1095-8657     ISO Abbreviation:  J. Struct. Biol.     Publication Date:  2013 Apr 
Date Detail:
Created Date:  2013-4-5     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9011206     Medline TA:  J Struct Biol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2013. Published by Elsevier Inc.
Rosetta Design Group LLC, Fairfax, VA 22030, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address:
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