EnGens : a computational framework for generation and analysis of representative protein conformational ensembles
Conev, Anja and Rigo, Mauricio Menegatti and Devaurs, Didier and Fonseca, André Faustino and Kalavadwala, Hussain and de Freitas, Martiela Vaz and Clementi, Cecilia and Zanatta, Geancarlo and Antunes, Dinler Amaral and Kavraki, Lydia E. (2023) EnGens : a computational framework for generation and analysis of representative protein conformational ensembles. Briefings in Bioinformatics, 24 (4). bbad242. ISSN 1467-5463 (https://doi.org/10.1093/bib/bbad242)
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Abstract
Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure determines its function, but this structure is not static, as proteins change their conformation to achieve various functions. Understanding the conformational landscapes of proteins is essential to understand their mechanism of action. Sets of carefully chosen conformations can summarize such complex landscapes and provide better insights into protein function than single conformations. We refer to these sets as representative conformational ensembles. Recent advances in computational methods have led to an increase in the number of available structural datasets spanning conformational landscapes. However, extracting representative conformational ensembles from such datasets is not an easy task and many methods have been developed to tackle it. Our new approach, EnGens (short for ensemble generation), collects these methods into a unified framework for generating and analyzing representative protein conformational ensembles. In this work, we: (1) provide an overview of existing methods and tools for representative protein structural ensemble generation and analysis; (2) unify existing approaches in an open-source Python package, and a portable Docker image, providing interactive visualizations within a Jupyter Notebook pipeline; (3) test our pipeline on a few canonical examples from the literature. Representative ensembles produced by EnGens can be used for many downstream tasks such as protein–ligand ensemble docking, Markov state modeling of protein dynamics and analysis of the effect of single-point mutations.
ORCID iDs
Conev, Anja, Rigo, Mauricio Menegatti, Devaurs, Didier ORCID: https://orcid.org/0000-0002-3415-9816, Fonseca, André Faustino, Kalavadwala, Hussain, de Freitas, Martiela Vaz, Clementi, Cecilia, Zanatta, Geancarlo, Antunes, Dinler Amaral and Kavraki, Lydia E.;-
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Item type: Article ID code: 90228 Dates: DateEvent7 July 2023Published10 June 2023AcceptedSubjects: Medicine > Biomedical engineering. Electronics. Instrumentation
Science > Mathematics > Electronic computers. Computer scienceDepartment: Faculty of Science > Computer and Information Sciences Depositing user: Pure Administrator Date deposited: 13 Aug 2024 14:26 Last modified: 01 Oct 2024 15:26 Related URLs: URI: https://strathprints.strath.ac.uk/id/eprint/90228