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Plos One : a Pareto-optimal Refinement Method for Protein Design Scaffolds, Volume 8

By Zhang, Yang

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Book Id: WPLBN0003942951
Format Type: PDF eBook :
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Reproduction Date: 2015

Title: Plos One : a Pareto-optimal Refinement Method for Protein Design Scaffolds, Volume 8  
Author: Zhang, Yang
Volume: Volume 8
Language: English
Subject: Journals, Science, Medical Science
Collections: Periodicals: Journal and Magazine Collection
Publication Date:
Publisher: Plos


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Zhang, Y. (n.d.). Plos One : a Pareto-optimal Refinement Method for Protein Design Scaffolds, Volume 8. Retrieved from

Description : Computational design of protein function involves a search for amino acids with the lowest energy subject to a set of constraints specifying function. In many cases a set of natural protein backbone structures, or ‘‘scaffolds’’, are searched to find regions where functional sites (an enzyme active site, ligand binding pocket, protein – protein interaction region, etc.) can be placed, and the identities of the surrounding amino acids are optimized to satisfy functional constraints. Input native protein structures almost invariably have regions that score very poorly with the design force field, and any design based on these unmodified structures may result in mutations away from the native sequence solely as a result of the energetic strain. Because the input structure is already a stable protein, it is desirable to keep the total number of mutations to a minimum and to avoid mutations resulting from poorly-scoring input structures. Here we describe a protocol using cycles of minimization with combined backbone/sidechain restraints that is Pareto-optimal with respect to RMSD to the native structure and energetic strain reduction. The protocol should be broadly useful in the preparation of scaffold libraries for functional site design.


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