The PTGL web server provides a database of protein secondary structure topologies [Schäfer et al., 2015, Bioinformatics; May et al., 2010, Nucleic Acids Res.; May et al., 2004, Bioinformatics]. It is based on protein-ligand graphs computed by the VPLG software. The PTGL uses a graph-based model to describe the structure of proteins on the super-secondary structure level.





This web server allows you to search for protein motifs which can be detected in the graphs. It also provides standardized 2D visualizations of protein graphs and folding graphs. In contrast to the manually curated CATH and SCOP databases, the method used by this server is fully automated. Similar servers, which also support substructure search, include ProSMoS and Pro-Origami.
SearchKey
Keyword search
Use the standard search form above to search protein topologies by keyword.
Enter PDB IDs like '7tim' or keywords known to relate to the biological macromolecules like 'kinase'
of interest and select the "Search" button.
Search Motifs
Search for topological protein structure motifs

Need help? See the user guide for a worked out motif search.


Alpha Motifs

Four Helix Bundle (?)
Globin Fold (?)

Beta Motifs

Up and Down Barrel (?)
Immunoglobulin Fold (?)
Beta Propeller (?)
Jelly Roll (?)
Complex graphs
Search for protein complexes

Need help? See the user guide for a worked out Complex Graph search.


Enter a query PDB ID, e.g., '4a97' to display complex information for that PDB file.


Custom linnot
Search for folding graph linear notation strings

Need help? See the user guide for a worked out linear notation search.


Select the graph type and notation, then enter a query linear notation string, e.g., '[e,10ae,-1ae,-7ae]'. Note that this searches the whole database and may take some minutes.

Search the notation of all graphs in the database for:
Random
Selects a few random protein chains to explore.
Selects and loads some random protein chains from the database.
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Introduction

PTGL stands for Protein Topology Graph Library. It is a database of protein structure topologies modeled as undirected, labeled graphs. It provides a web server to visualize and analyze protein structure topologies at different scales, e.g., secondary structure level and chain level. The graph computation was done by our software Visualization of Protein-Ligand Graphs (VPLG). VPLG is based on the 3D atomic coordinates from the PDB either as legacy PDB file or as macromolecular Crystallographic Information File (mmCIF). Reading mmCIFs allows processing large protein structures (> 62 chains or > 99,999 atoms). The secondary structure assignment is parsed with small adaptions from a DSSP file.

Read more about PTGL...
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User Guide

You can find worked out step-by-step examples with screenshots of the output of the following topics:

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