TMKit: a Python interface for computational analysis of transmembrane proteins

Author:

Sun Jianfeng1ORCID,Kulandaisamy Arulsamy2,Ru Jinlong3ORCID,Gromiha M Michael2ORCID,Cribbs Adam P1ORCID

Affiliation:

1. University of Oxford Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, Botnar Research Centre, , Headington, Oxford OX3 7LD , UK

2. Indian Institute of Technology Madras Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, , Chennai 600036, Tamil Nadu , India

3. Technical University of Munich Chair of Prevention of Microbial Diseases, School of Life Sciences Weihenstephan, , 85354 Freising , Germany

Abstract

Abstract Transmembrane proteins are receptors, enzymes, transporters and ion channels that are instrumental in regulating a variety of cellular activities, such as signal transduction and cell communication. Despite tremendous progress in computational capacities to support protein research, there is still a significant gap in the availability of specialized computational analysis toolkits for transmembrane protein research. Here, we introduce TMKit, an open-source Python programming interface that is modular, scalable and specifically designed for processing transmembrane protein data. TMKit is a one-stop computational analysis tool for transmembrane proteins, enabling users to perform database wrangling, engineer features at the mutational, domain and topological levels, and visualize protein–protein interaction interfaces. In addition, TMKit includes seqNetRR, a high-performance computing library that allows customized construction of a large number of residue connections. This library is particularly well suited for assigning correlation matrix-based features at a fast speed. TMKit should serve as a useful tool for researchers in assisting the study of transmembrane protein sequences and structures. TMKit is publicly available through https://github.com/2003100127/tmkit and https://tmkit-guide.herokuapp.com/doc/overview.

Funder

Medical Research Council

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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