References of "Koch, Ina"
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See detailThe new Protein Topology Graph Library web server
Schäfer, Tim; Bruneß, Daniel; Scheck, Andreas et al

in Bioinformatics (2016), 32(3), 474-6

Summary: We present a new, extended version of the Protein Topology Graph Library (PTGL) web server. The PTGL describes the protein topology on the super-secondary structure level. It allows to compute ... [more ▼]

Summary: We present a new, extended version of the Protein Topology Graph Library (PTGL) web server. The PTGL describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements (SSEs), increased usability, and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. Availability: The PTGL server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. [less ▲]

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See detailHierarchical representation of supersecondary structures using a graph-theoretical approach.
Koch, Ina; Kreuchwig, Annika; May, Patrick UL

in Methods in Molecular Biology (2013), 932

The unique representation of proteins becomes more and more important with the growing number of known protein structure data. Graph-theory provides many methods not only for the description but also for ... [more ▼]

The unique representation of proteins becomes more and more important with the growing number of known protein structure data. Graph-theory provides many methods not only for the description but also for comparison and classification of protein structures. Here, we describe a graph-theoretical modeling approach of the protein supersecondary structure. The resulting linear notations are intuitive and can be used to find common substructures very fast and easily. We illustrate the necessary definitions by biological examples and discuss the representation of various supersecondary structure motifs. [less ▲]

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See detailComputation and Visualization of Protein Topology Graphs Including Ligand Information
Schäfer, Tim; May, Patrick UL; Koch, Ina

in Böcker, Sebasttian; Hufsky, Franziska; Scheubert, Kerstin (Eds.) et al German Conference on Bioinformatics 2012 (2012)

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See detailPTGL: a database for secondary structure-based protein topologies.
May, Patrick UL; Kreuchwig, Annika; Steinke, Thomas et al

in Nucleic Acids Research (2010), 38(Database issue), 326-30

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 ... [more ▼]

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. [less ▲]

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See detailJProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information
Scheer, Maurice; Klawonn, Frank; Münch, Richard et al

in Nucleic Acids Research (2006)

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See detailPTGL--a web-based database application for protein topologies.
May, Patrick UL; Barthel, Stefan; Koch, Ina

in Bioinformatics (2004), 20(17), 3277-9

Protein Topology Graph Library (PTGL) is a database application for the representation and retrieval of protein topologies. Protein topologies are based on a graph-theoretical protein model at secondary ... [more ▼]

Protein Topology Graph Library (PTGL) is a database application for the representation and retrieval of protein topologies. Protein topologies are based on a graph-theoretical protein model at secondary structure level. Different views on protein topology are given by four linear notations for their characterization. Protein topologies can be derived at different description levels considering alpha- and beta-structures. The on-line search tool is based on an object-relational database and provides a query browser for data interrogation by string patterns, keyword queries and sequence similarity. Protein topologies are represented both as schematic diagrams and as three-dimensional images. [less ▲]

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