PurificationDB: database of purification conditions for proteins
Author:
Garland Olivia1ORCID,
Radaeva Mariia1,
Pandey Mohit1,
Cherkasov Artem1,
Lallous Nada1ORCID
Affiliation:
1. Vancouver Prostate Centre, University of British Columbia , 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
Abstract
AbstractThe isolation of proteins of interest from cell lysates is an integral step to study protein structure and function. Liquid chromatography is a technique commonly used for protein purification, where the separation is performed by exploiting the differences in physical and chemical characteristics of proteins. The complex nature of proteins requires researchers to carefully choose buffers that maintain stability and activity of the protein while also allowing for appropriate interaction with chromatography columns. To choose the proper buffer, biochemists often search for reports of successful purification in the literature; however, they often encounter roadblocks such as lack of accessibility to journals, non-exhaustive specification of components and unfamiliar naming conventions. To overcome such issues, we present PurificationDB (https://purificationdatabase.herokuapp.com/), an open-access and user-friendly knowledge base that contains 4732 curated and standardized entries of protein purification conditions. Buffer specifications were derived from the literature using named-entity recognition techniques developed using common nomenclature provided by protein biochemists. PurificationDB also incorporates information associated with well-known protein databases: Protein Data Bank and UniProt. PurificationDB facilitates easy access to data on protein purification techniques and contributes to the growing effort of creating open resources that organize experimental conditions and data for improved access and analysis.Database URL https://purificationdatabase.herokuapp.com/
Funder
Canadian Institute of Health Research
DoD
Canadian Institutes of Health Research
Publisher
Oxford University Press (OUP)
Subject
General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Information Systems
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