License: Creative Commons Attribution-NoDerivs 3.0 Unported license (CC BY-ND 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/OASIcs.GCB.2012.108
URN: urn:nbn:de:0030-drops-37226
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Schäfer, Tim ; May, Patrick ; Koch, Ina

Computation and Visualization of Protein Topology Graphs Including Ligand Information

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Motivation: Ligand information is of great interest to understand protein function. Protein structure topology can be modeled as a graph with secondary structure elements as vertices and spatial contacts between them as edges. Meaningful representations of such graphs in 2D are required for the visual inspection, comparison and analysis of protein folds, but their automatic visualization is still challenging. We present an approach which solves this task, supports different graph types and can optionally include ligand contacts.

Results: Our method extends the field of protein structure description and visualization by including ligand information. It generates a mathematically unique representation and high- quality 2D plots of the secondary structure of a protein based on a protein-ligand graph. This graph is computed from 3D atom coordinates in PDB files and the corresponding SSE assignments of the DSSP algorithm. The related software supports different notations and allows a rapid visualization of protein structures. It can also export graphs in various standard file formats so they can be used with other software. Our approach visualizes ligands in relationship to protein structure topology and thus represents a useful tool for exploring protein structures.

Availability: The software is released under an open source license and available at in the Software section under Visualization of Protein Ligand Graphs.

BibTeX - Entry

  author =	{Tim Sch{\"a}fer and Patrick May and Ina Koch},
  title =	{{Computation and Visualization of Protein Topology Graphs Including Ligand Information}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{108--118},
  series =	{OpenAccess Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{Sebastian B{\"o}cker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{},
  URN =		{urn:nbn:de:0030-drops-37226},
  doi =		{10.4230/OASIcs.GCB.2012.108},
  annote =	{Keywords: protein structure, graph theory, ligand, secondary structure, protein ligang graph}

Keywords: protein structure, graph theory, ligand, secondary structure, protein ligang graph
Collection: German Conference on Bioinformatics 2012
Issue Date: 2012
Date of publication: 13.09.2012

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