EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

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dc.citation.articleNumberbbad242
dc.citation.issueNumber4
dc.citation.journalTitleBriefings in Bioinformatics
dc.citation.volumeNumber24
dc.contributor.authorConev, Anja
dc.contributor.authorRigo, Mauricio Menegatti
dc.contributor.authorDevaurs, Didier
dc.contributor.authorFonseca, André Faustino
dc.contributor.authorKalavadwala, Hussain
dc.contributor.authorde Freitas, Martiela Vaz
dc.contributor.authorClementi, Cecilia
dc.contributor.authorZanatta, Geancarlo
dc.contributor.authorAntunes, Dinler Amaral
dc.contributor.authorKavraki, Lydia E
dc.date.accessioned2023-08-01T17:29:48Z
dc.date.available2023-08-01T17:29:48Z
dc.date.issued2023
dc.description.abstractProteins 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.
dc.identifier.citationConev, Anja, Rigo, Mauricio Menegatti, Devaurs, Didier, et al.. "EnGens: a computational framework for generation and analysis of representative protein conformational ensembles." <i>Briefings in Bioinformatics,</i> 24, no. 4 (2023) Oxford University Press: https://doi.org/10.1093/bib/bbad242.
dc.identifier.digitalbbad242
dc.identifier.doihttps://doi.org/10.1093/bib/bbad242
dc.identifier.urihttps://hdl.handle.net/1911/115042
dc.language.isoeng
dc.publisherOxford University Press
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution-NonCommercial (CC BY-NC) license.  Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of Fair Use or other exemptions to copyright law must be obtained from the copyright holder.
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.titleEnGens: a computational framework for generation and analysis of representative protein conformational ensembles
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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