TMKit: a Python interface for computational analysis of transmembrane proteins.
Brief Bioinform
; 24(5)2023 09 20.
Article
em En
| MEDLINE
| ID: mdl-37594311
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.
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1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Biologia Computacional
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article