title: Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins.
abstract: An algorithmic method for drawing residue-based schematic diagrams of proteins on a 2D page is presented and illustrated. The method allows the creation of rendering engines dedicated to a given family of sequences, or fold. The initial implementation provides an engine that can produce a 2D diagram representing secondary structure for any transmembrane protein sequence. We present the details of the strategy for automating the drawing of these diagrams. The most important part of this strategy is the development of an algorithm for laying out residues of a loop that connects to arbitrary points of a 2D plane. As implemented, this algorithm is suitable for real-time modification of the loop layout. This work is of interest for the representation and analysis of data from (1) protein databases, (2) mutagenesis results, or (3) various kinds of protein context-dependent annotations or data.
authors.affiliation: Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029-6574, USA. campagne@inka.mssm.edu
authors.forename: F
authors.initials: F
authors.lastname: Campagne
authors.forename: H
authors.initials: H
authors.lastname: Weinstein
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D019992:Databases as Topic; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016296:Mutagenesis; D017510:Protein Folding; D017433:Protein Structure, Secondary; D018909:src Homology Domains
chemical_list: D008565:Membrane Proteins