ABC-finder: A containerized web server for the identification and topology prediction of ABC proteins

Poonam Vishwakarma; Naveen Kumar Meena; Rajendra Prasad; Andrew M Lynn; Atanu Banerjee

doi:10.1016/j.bbamem.2021.183640

ABC-finder: A containerized web server for the identification and topology prediction of ABC proteins

Biochim Biophys Acta Biomembr. 2021 Aug 1;1863(8):183640. doi: 10.1016/j.bbamem.2021.183640. Epub 2021 May 3.

Authors

Poonam Vishwakarma¹, Naveen Kumar Meena¹, Rajendra Prasad², Andrew M Lynn³, Atanu Banerjee⁴

Affiliations

¹ School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
² Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India. Electronic address: rprasad@ggn.amity.edu.
³ School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India. Electronic address: andrew@jnu.ac.in.
⁴ Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India. Electronic address: abanerjee1@ggn.amity.edu.

PMID: 33957109
DOI: 10.1016/j.bbamem.2021.183640

Abstract

In view of the multiple clinical and physiological implications of ABC transporter proteins, there is a considerable interest among researchers to characterize them functionally. However, such characterizations are based on the premise that ABC proteins are accurately identified in the proteome of an organism, and their topology is correctly predicted. With this objective, we have developed ABC-finder, i.e., a Docker-based package for the identification of ABC proteins in all organisms, and visualization of the topology of ABC proteins using a web browser. ABC-finder is built and deployed in a Linux container, making it scalable for many concurrent users on our servers and enabling users to download and run it locally. Overall, ABC-finder is a convenient, portable, and platform-independent tool for the identification and topology prediction of ABC proteins. ABC-finder is accessible at http://abc-finder.osdd.jnu.ac.in.

Keywords: ABC proteins; Docker; Nucleotide-binding domains; Reproducibility; Transmembrane domains.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

ATP-Binding Cassette Transporters / classification
ATP-Binding Cassette Transporters / genetics*
ATP-Binding Cassette Transporters / isolation & purification
Animals
Humans
Internet
Proteome / genetics*
Software*

Substances

ATP-Binding Cassette Transporters
Proteome