Building protein diagrams on the web with the residue-based diagram editor RbDe

Nucleic Acids Res. 2003 Jul 1;31(13):3856-8. doi: 10.1093/nar/gkg552.

Abstract

The residue-based diagram editor (RbDe) is web-based software that greatly simplifies the construction of schematic diagrams of proteins. Residue-based diagrams display the sequence of a given protein in the context of its secondary and tertiary structure. Such diagrams are frequently used to summarize mutations or sequence features, in the context of the overall topology of a protein. The initial version of RbDe was designed for transmembrane proteins and has enabled many users to create diagrams of large systems such as G protein-coupled receptors or transporters. We present an extended diagram editor that supports other families of proteins. Users can now import custom-diagram layouts, use them to render members of any protein family and generate high-quality output for publication purposes. RbDe is available free over the web, at http://icb.mssm.edu/crt/RbDe

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Calmodulin / chemistry
  • Computer Graphics
  • Humans
  • Internet
  • Membrane Proteins / chemistry*
  • Membrane Transport Proteins / chemistry
  • Models, Molecular*
  • Protein Conformation
  • Proteins / chemistry*
  • Software*
  • User-Computer Interface

Substances

  • Calmodulin
  • Membrane Proteins
  • Membrane Transport Proteins
  • Proteins

Associated data

  • PDB/1A29
  • PDB/3CLN