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EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry

View ORCID ProfileAntoniya A. Aleksandrova, View ORCID ProfileEdoardo Sarti, View ORCID ProfileLucy R. Forrest
doi: https://doi.org/10.1101/391961
Antoniya A. Aleksandrova
Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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  • ORCID record for Antoniya A. Aleksandrova
Edoardo Sarti
Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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Lucy R. Forrest
Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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  • For correspondence: lucy.forrest@nih.gov
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Summary

Protein structure determination and prediction, active site detection, and protein sequence alignment techniques all exploit information about protein structure and structural relationships. For membrane proteins, however, there is no agreement among available online tools for highlighting and mapping such structural similarities. Moreover, no available resource provides a systematic overview of quaternary and internal symmetries, and their orientation with respect to the membrane, despite the fact that these properties can provide key insights into membrane protein function. To address these issues, we created the Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry (EncoMPASS), a database for relating integral membrane proteins of known structure from the points of view of sequence, structure, and symmetry. EncoMPASS is accessible at https://encompass.ninds.nih.gov and its contents can be easily downloaded. This allows the user not only to focus on specific systems, but also to study general properties of the structure and evolution of membrane proteins.

Highlights

  • -EncoMPASS relates and analyzes known structures of membrane proteins

  • -Structure and sequence similarity is assessed through alignments and topology considerations, not clustering

  • -Symmetry is detected based on CE-Symm and SymD using a multi-step procedure

Abbreviations
TM
transmembrane
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Posted August 15, 2018.
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EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry
Antoniya A. Aleksandrova, Edoardo Sarti, Lucy R. Forrest
bioRxiv 391961; doi: https://doi.org/10.1101/391961
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EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry
Antoniya A. Aleksandrova, Edoardo Sarti, Lucy R. Forrest
bioRxiv 391961; doi: https://doi.org/10.1101/391961

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