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PDB Downloader

StreamableVernalis PDB Connector KNIME nodes package version 1.27.2.v202010191232 by Vernalis (R&D), UK

This node, and the corresponding source node, allows the downloading of structure and sequence files from the RCSB PDB . The formats supported are (not all formats are available for all structures!):
  • PDB
  • mmCIF
  • Structure Factors
  • PDBML
  • FASTA Format Sequence
  • NMR Restraints
  • NMR Restraints v2
  • NMR Chemical Shifts
PDB files are cast as PDB cells, and PDBML as XML cells. No checking the the structure IDs is carried out - invalid IDs will return cells containing missing values. WARNING - the PDBML option can result in very large tables!

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

Options

Select a column containing the PDB IDs
Select a String column containing a list of PDB IDs
Downloaded Files
Select the desired file format(s) from the available options
Select All
Selects all options in the Downloaded Files option list
Clear
Clears the selection and returns it to the default (PDB only) selection

Input Ports

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Input Data table containing a list of PDB IDs

Output Ports

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Output table with downloaded file(s) appended

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.2

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

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Developers

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