title: Normalization of nomenclature for peptide motifs as ligands of modular protein domains.
abstract: We propose a normalization of symbols and terms used to describe, accurately and succinctly, the detailed interactions between amino acid residues of pairs of interacting proteins at protein:protein (or protein:peptide) interfaces. Our aim is to unify several diverse descriptions currently in use in order to facilitate communication in the rapidly progressing field of signaling by protein domains. In order for the nomenclature to be convenient and widely used, we also suggest a parallel set of symbols restricted to the ASCII format allowing accurate parsing of the nomenclature to a computer-readable form. This proposal will be reviewed in the future and will therefore be open for the inclusion of new rules, modifications and changes.
authors.affiliation: Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway. aasland@mbi.uib.no
authors.forename: Rein
authors.initials: R
authors.lastname: Aasland
authors.forename: Charles
authors.initials: C
authors.lastname: Abrams
authors.forename: Christophe
authors.initials: C
authors.lastname: Ampe
authors.forename: Linda J
authors.initials: LJ
authors.lastname: Ball
authors.forename: Mark T
authors.initials: MT
authors.lastname: Bedford
authors.forename: Gianni
authors.initials: G
authors.lastname: Cesareni
authors.forename: Mario
authors.initials: M
authors.lastname: Gimona
authors.forename: James H
authors.initials: JH
authors.lastname: Hurley
authors.forename: Thomas
authors.initials: T
authors.lastname: Jarchau
authors.forename: Veli Pekka
authors.initials: VP
authors.lastname: Lehto
authors.forename: Mark A
authors.initials: MA
authors.lastname: Lemmon
authors.forename: Rune
authors.initials: R
authors.lastname: Linding
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Mayer
authors.forename: Makoto
authors.initials: M
authors.lastname: Nagai
authors.forename: Marius
authors.initials: M
authors.lastname: Sudol
authors.forename: Ulrich
authors.initials: U
authors.lastname: Walter
authors.forename: Steve J
authors.initials: SJ
authors.lastname: Winder
mesh_terms: D001665:Binding Sites; D008024:Ligands; D010455:Peptides / Q000737:chemistry* / Q000145:classification; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D009626:Terminology as Topic; D018909:src Homology Domains
chemical_list: D008024:Ligands; D010455:Peptides; D011506:Proteins