ProtaBank: A repository for protein design and engineering data

被引:41
|
作者
Wang, Connie Y. [1 ]
Chang, Paul M. [1 ]
Ary, Marie L. [1 ]
Allen, Benjamin D. [1 ,2 ,3 ]
Chica, Roberto A. [4 ]
Mayo, Stephen L. [1 ,5 ,6 ]
Olafson, Barry D. [1 ]
机构
[1] Protabit LLC, 129 N Hill Ave,Suite 102, Pasadena, CA 91106 USA
[2] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA
[3] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
[4] Univ Ottawa, Dept Chem & Biomol Sci, Ottawa, ON K1N 6N5, Canada
[5] CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA
[6] CALTECH, Div Chem & Chem Engn, Pasadena, CA 91125 USA
基金
美国国家卫生研究院;
关键词
protein engineering; protein design; relational database; protein mutants; data resource; protein stability; data sets; IMMUNOGLOBULIN BINDING DOMAIN; CRYSTAL-STRUCTURE; BETA-LACTAMASE; STABILITY; OPTIMIZATION; GENERATION; AFFINITY; MUTANTS; GENE;
D O I
10.1002/pro.3406
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at .
引用
收藏
页码:1113 / 1124
页数:12
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