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PDB Connector Query Builder

Vernalis PDB Connector KNIME nodes package version 1.30.1.v202103301200 by Vernalis (R&D), UK

This node provides access to the RCSB PDB advanced query webservice, in an interface which closely follows the web UI at http://www.rcsb.org/search/advanced Queries comprise nested fields and subgroups (which themselves can contain fields / subgroups to an arbitrary depth). The items in each field are combined using the indicated logic operator

Fields can be removed by clicking on the 'X' button at the left-hand side of the field, and added by clicking the 'Add Field' button at the bottom of the relevant group.

Subgroups can be added by clicking the 'Add SubGroup' button at the bottom of the relevant parent group panel, and removed by clicking the 'Remove Group' button at the bottom of the subgroup. The top-most 'parent' group cannot be removed, although it can be left empty.

Individual fields can be reset by clicking the 'Clear' button at the right-hand side of the field. Clicking on the 'Clear' button at the bottom of a subgroup panel removes all fields and subgroups from that panel

Queries can be tested by pressing the 'Count' button, either at the right-hand side of the field or the bottom of the group panel. In either case, the button text is replaced with the count for the relevant part of the query (field, subgroup or entire query). The button remains unavailable for repeated counting until the query it relates to is changed in some way.

Many of the input boxes will provide live drop-downs of possible options once text entry has started.

The relationship between Text, Structure and Sequence queries is always 'AND'

This node was developed by Vernalis Research (Cambridge, UK) . For feedback and more information, please contact knime@vernalis.com

Options

Attribute Query

Query Type
The type of query - clicking on the text box produces a hierarchical menu to choose from. See above for description of the button behaviours

Structure & Sequence Query

Sequence Motif
Search for small sequence motifs. Enter the sequence motif query in either simple, PROSITE or regex format. To see the motif matching information, select 'Polymer Entities' from the result type dropdown in the 'PDB Connector Execute Query' node
Sequence
Search sequences using the mmseqs2 method. To see E-value, Sequence Identity and region information, select 'Polymer Entities' from the result type dropdown in the 'PDB Connector Execute Query' node
Structure Similarity
Search protein structure shapes using the BioZernike algorithm (Guzenko et al., 2020). To see the structure match score, select 'Assemblies' from the result type dropdown in the 'PDB Connector Execute Query' node

Chemical

Perform chemical ligand searches

Chemical Query
The Query Value to search on
Query Type
The Type of Query
Descriptor Type
The type of descriptor to use
Match Type
The type of matching to perform

Output Ports

Icon
The PDB Query

Workflows

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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