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          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents



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ID: 539706.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
PTGL : a database for secondary structure-based protein topologies
Authors:May, P.; Kreuchwig, A.; Steinke, T.; Koch, I.
Language:English
Date of Publication (YYYY-MM-DD):2010-01
Title of Journal:Nucleic Acids Research
Journal Abbrev.:Nucleic Acids Res
Volume:38
Issue / Number:Database issue
Start Page:D326
End Page:30
Copyright:© 2010 Oxford University Press
Review Status:not specified
Audience:Experts Only
Abstract / Description:With growing amount of experimental data, the number of known protein structures also increases continuously. Classification of protein structures helps to understand relationships between protein structure and function. The main classification methods based on secondary structures are SCOP, CATH and TOPS, which all classify under different aspects, and therefore can lead to different results. We developed a mathematically unique representation of protein structure topologies at a higher abstraction level providing new aspects of classification and enabling for a fast search through the data. Protein Topology Graph Library (PTGL; http://ptgl.zib.de) aims at providing a database on protein secondary structure topologies, including search facilities, the visualization as intuitive topology diagrams as well as in the 3D structure, and additional information. Secondary structure-based protein topologies are represented uniquely as undirected labeled graphs in four different ways allowing for exploration under different aspects. The linear notations, and the 2D and 3D diagrams of each notation facilitate a deeper understanding of protein topologies. Several search functions for topologies and sub-topologies, BLAST search possibility, and links to SCOP, CATH and PDBsum support individual and large-scale investigation of protein structures. Currently, PTGL comprises topologies of 54,859 protein structures. Main structural patterns for common structural motifs like TIM-barrel or Jelly Roll are pre-implemented, and can easily be searched.
Free Keywords:Amino Acid Motifs; Animals; Computational Biology/*methods/trends; Computer Graphics; Crystallography, X-Ray/methods; *Databases, Genetic; *Databases, Protein; Humans; Information Storage and Retrieval/methods; Internet; Protein Conformation; *Protein Structure, Secondary; Proteins/*chemistry; Software
External Publication Status:published
Document Type:Article
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
MPI für molekulare Pflanzenphysiologie
External Affiliations:Leibniz-Institut fuer Molekulare Pharmakologie, Structural Bioinformatics, Robert-Roessle-Strasse 10, 13125
Berlin
Zuse Institute Berlin, Computer Science Research, Takustrasse 7, 14195 Berlin
Beuth University for Technology Berlin, FB VI, Bioinformatics, Seestrasse 64, 13347 Berlin
Identifiers:ISSN:1362-4962 (Electronic) 0305-1048 (Linking) %R gkp9... [ID No:1]
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=... [ID No:2]
DOI:doi:10.1093/nar/gkp980
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