SecStrAPI

version 1.0

SecStrAPI is a service providing annotation of secondary structure elements in protein structures.

Annotation of Secondary Structure Elements /Annotation/<pdbId>
Returns a JSON response with the list of annotated secondary structure elements for the specified PDB entry.

Examples

/Annotation/1tqn

Parameters

NameDescription
pdbId PDB ID of the entry (e.g. 1tqn).

Output Details

The response format is explained here.

Extras

FileDescription
secstrapi_plugin-1.4.py This PyMOL plugin can be used to download annotations from this API and visualize them directly in PyMOL. Install via Plugin Manager or type run https://webchem.ncbr.muni.cz/API/SecStr/Downloads/secstrapi_plugin.py.
Example of usage:
annotate_sec_str 1og5 and chain A
(Fetches the structure of 1og5 and annotates its chain A using annotation from SecStrAPI.)
annotate_sec_str 1og5 and chain A, my_annotations/1og5.sses.json
(Does the same, but uses annotation from the specified file instead of the one from SecStrAPI.)
annotate_sec_str 1og5A
(Fetches the structure of 1og5 and annotates domain 1og5A (~ chain A).)
SecStrAPI-CytochromesP450-20200707.zip All available annotations

List of Available Annotations /List/Annotation
Returns a JSON response with PDB IDs for which a secondary structure annotation is available.

Examples

/List/Annotation

Output Details

Response is a JSON object in which the keys are PDB IDs and the values are lists of domains that are annotated for each PDB ID.
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SecStrAPI is a part of services provided by ELIXIR – European research infrastructure for biological information. For other services provided by ELIXIR's Czech Republic Node visit www.elixir-czech.cz/services.
© 2017 – now, Adam Midlik