scholarly journals ProtaBank: A repository for protein design and engineering data

2018 ◽  
Vol 27 (6) ◽  
pp. 1113-1124 ◽  
Author(s):  
Connie Y. Wang ◽  
Paul M. Chang ◽  
Marie L. Ary ◽  
Benjamin D. Allen ◽  
Roberto A. Chica ◽  
...  
Keyword(s):  
Protein Design ◽  
Engineering Data ◽  
Protein Design And Engineering

scholarly journals ProtaBank: A repository for protein design and engineering data

2019 ◽  
Vol 28 (3) ◽  
pp. 672-672
Author(s):  
Connie Y. Wang ◽  
Paul M. Chang ◽  
Marie L. Ary ◽  
Benjamin D. Allen ◽  
Roberto A. Chica ◽  
...  
Keyword(s):  
Protein Design ◽  
Engineering Data ◽  
Protein Design And Engineering

scholarly journals ProtaBank: A repository for protein design and engineering data

2018 ◽  
Author(s):  
Connie Y. Wang ◽  
Paul M. Chang ◽  
Marie L. Ary ◽  
Benjamin D. Allen ◽  
Roberto A. Chica ◽  
...  
Keyword(s):  
Protein Engineering ◽  
Protein Design ◽  
Local Alignment ◽  
Data Sets ◽  
Standard Format ◽  
Predictive Tools ◽  
Engineering Data ◽  
Schema Design ◽  
Wide Range ◽  
Protein Design And Engineering

AbstractWe 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 https://protabank.org.ImpactThe ProtaBank database provides a central repository for researchers to store, query, analyze, and share all types of protein engineering data. This modern database will serve a pivotal role in organizing protein engineering data and leveraging the increasingly large amounts of mutational data being generated. Together with the analysis tools, it will help scientists gain insights into sequence-function relationships, support the development of new predictive tools and algorithms, and facilitate future protein engineering efforts.Abbreviations3Dthree-dimensionalAPIapplication programming interfaceAWSAmazon Web ServicesBLASTBasic Local Alignment Search ToolCmconcentration of denaturant at midpoint of unfolding transitionCSVcomma-separated valuesΔGGibbs free energy of folding/unfoldingGβ1β1 domain of Streptococcal protein GGdmClguanidinium chloridekcatcatalytic rate constantKddissociation constantMICminimum inhibitory concentrationPDBProtein Data BankPEprotein engineeringRDSRelational Database ServicesRESTRepresentation State TransferTmmelting temperature

Fluorinated amino acids in protein design and engineering

2002 ◽  
Vol 31 (6) ◽  
pp. 335-341 ◽  
Author(s):  
Nicholas C. Yoder ◽  
Krishna Kumar
Keyword(s):  
Amino Acids ◽  
Protein Design ◽  
Fluorinated Amino Acids ◽  
Protein Design And Engineering

scholarly journals Evolution of fold switching in a metamorphic protein

Science ◽  
2020 ◽  
Vol 371 (6524) ◽  
pp. 86-90
Author(s):  
Acacia F. Dishman ◽  
Robert C. Tyler ◽  
Jamie C. Fox ◽  
Andrew B. Kleist ◽  
Kenneth E. Prehoda ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Protein Design ◽  
Structural Constraints ◽  
Ancestral Reconstruction ◽  
Dimer Interface ◽  
Multiple Structures ◽  
Metamorphic Protein ◽  
Equal Population ◽  
Chemokine Family ◽  
Protein Design And Engineering

Metamorphic proteins switch between different folds, defying the protein folding paradigm. It is unclear how fold switching arises during evolution. With ancestral reconstruction and nuclear magnetic resonance, we studied the evolution of the metamorphic human protein XCL1, which has two distinct folds with different functions, making it an unusual member of the chemokine family, whose members generally adopt one conserved fold. XCL1 evolved from an ancestor with the chemokine fold. Evolution of a dimer interface, changes in structural constraints and molecular strain, and alteration of intramolecular protein contacts drove the evolution of metamorphosis. Then, XCL1 likely evolved to preferentially populate the noncanonical fold before reaching its modern-day near-equal population of folds. These discoveries illuminate how one sequence has evolved to encode multiple structures, revealing principles for protein design and engineering.

Fluoroprolines as Tools for Protein Design and Engineering

2001 ◽  
Vol 40 (5) ◽  
pp. 923-925 ◽  
Author(s):  
Christian Renner ◽  
Stefan Alefelder ◽  
Jae H. Bae ◽  
Nediljko Budisa ◽  
Robert Huber ◽  
...  
Keyword(s):  
Protein Design ◽  
Protein Design And Engineering

scholarly journals A New Tool for Custom Protein Design and Engineering - DH10 Bac-TAG

2016 ◽  
Vol 110 (3) ◽  
pp. 345a
Author(s):  
Christine Koehler ◽  
Paul Sauter ◽  
Mirella Wawryszyn ◽  
Gemma Estrada Girona ◽  
Markus H. Fritz ◽  
...  
Keyword(s):  
Protein Design ◽  
Protein Design And Engineering
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