Aleksandrova, A. A. | bioRxiv Science

bioRxiv2019

MemSTATS: A Benchmark Set of Membrane Protein Symmetries and Pseudo-Symmetries

In membrane proteins, symmetry and pseudo-symmetry often have functional or evolutionary implications. However, available symmetry detection methods have not been tested systematically on this class of proteins due to the lack of an appropriate benchmark set. Here we present MemSTATS, a publicly-available benchmark set of both quaternary and internal symmetries in membrane protein structures described in terms of order, repeated elements, and orientation of the axis with respect to the membrane plane. Moreover, using MemSTATS, we compare the performance of four widely-used symmetry detection algorithms and highlight specific challenges and areas for improvement in the future.

bioinformatics↗

bioRxiv2018

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

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.\n\nHighlights-EncoMPASS relates and analyzes known structures of membrane proteins\n-Structure and sequence similarity is assessed through alignments and topology considerations, not clustering\n-Symmetry is detected based on CE-Symm and SymD using a multi-step procedure

bioinformatics↗