Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins. Academic Article uri icon

Overview

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.

publication date

  • January 1, 1999

Research

keywords

  • Membrane Proteins
  • Protein Structure, Secondary

Identity

Scopus Document Identifier

  • 0033497867

Digital Object Identifier (DOI)

  • 10.1016/s1093-3263(99)00032-7

PubMed ID

  • 10736778

Additional Document Info

volume

  • 17

issue

  • 3-4