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

Abstract

SummaryProtein 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 theEncyclopediaofMembraneProteinsAnalyzed byStructure 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 athttps://encompass.ninds.nih.govand 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