title: Membrane positioning for high- and low-resolution protein structures through a binary classification approach.
abstract: The critical importance of algorithms for orienting proteins in the lipid bilayer stems from the extreme difficulty in obtaining experimental data about the membrane boundaries. Here, we present a computational method for positioning protein structures in the membrane, based on the sole alpha carbon coordinates and, therefore, compatible with both high and low structural resolutions. Our algorithm follows a new and simple approach, by treating the membrane assignment problem as a binary classification. Compared with the state-of-the-art algorithms, our method achieves similar accuracy, while being faster. Finally, our open-source software is also capable of processing coarse-grained models of protein structures.
authors.affiliation: Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France guillaume.postic@univ-paris-diderot.fr jean-christophe.gelly@univ-paris-diderot.fr.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Postic
authors.affiliation: Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France.
authors.forename: Yassine
authors.initials: Y
authors.lastname: Ghouzam
authors.affiliation: Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Guiraud
authors.affiliation: Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France guillaume.postic@univ-paris-diderot.fr jean-christophe.gelly@univ-paris-diderot.fr.
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Gelly
mesh_terms: D000465:Algorithms; D002244:Carbon / Q000737:chemistry; D002462:Cell Membrane / Q000737:chemistry*; D019295:Computational Biology; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D013997:Time Factors
chemical_list: D008565:Membrane Proteins; D002244:Carbon
keywords: binary classification; coarse-grained models; lipid bilayer assignment; low-resolution structures; membrane proteins