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01_​PDB_​Query_​Download_​and_​Save_​Locally

PDB Query and download

This workflow demonstrates how to connect to the Protein Data Bank (PDB) using KNIME nodes. In the first section, the new PDB Connector nodes are used to build a query and generate a custom report. The PDB Downloader node is the used to save local copies.
The last section shows an example of how to load and perform operations on local files.

Execute this workflow to build and execute query using PDB nodes. Results are then saved andused locally. Webservice query and downloads from PDB at www.rcsb.org Handle some local PDB files - Some of the information extracted is also available in the reporttable from the 'PDB Connector Custom Report' node Create a local pathto save downloads toSave a localcopy of the pdb filesExtract someproperties from the filesProcess the FASTAdata to Chains& SequencesLoad local PDBfilesBuild a query forAuthor=Roughley, S.D.Run the queryat rcsb.orgDownload resultsin PDB format andFASTA sequencesfrom rcsb.orgGet a structure reportfrom rcsb.orgGet the observed and database sequencesfrom the PDB file Java Snippet(simple) PDB Saver PDB PropertyExtractor FASTA SequenceExtractor PDB Loader Create TEMP dir PDB Connector XMLQuery Builder PDB Connector QueryOnly (XML Query) PDB Downloader PDB ConnectorCustom Report PDB SequenceExtractor List Files Execute this workflow to build and execute query using PDB nodes. Results are then saved andused locally. Webservice query and downloads from PDB at www.rcsb.org Handle some local PDB files - Some of the information extracted is also available in the reporttable from the 'PDB Connector Custom Report' node Create a local pathto save downloads toSave a localcopy of the pdb filesExtract someproperties from the filesProcess the FASTAdata to Chains& SequencesLoad local PDBfilesBuild a query forAuthor=Roughley, S.D.Run the queryat rcsb.orgDownload resultsin PDB format andFASTA sequencesfrom rcsb.orgGet a structure reportfrom rcsb.orgGet the observed and database sequencesfrom the PDB fileJava Snippet(simple) PDB Saver PDB PropertyExtractor FASTA SequenceExtractor PDB Loader Create TEMP dir PDB Connector XMLQuery Builder PDB Connector QueryOnly (XML Query) PDB Downloader PDB ConnectorCustom Report PDB SequenceExtractor List Files

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
On NodePit since: 2019-07-12
Last update: 2026-07-19
Created with KNIME version: v4.1.0
Tags: PDBConnectorPDB Advanced QueryPDB Custom ReportRCSB PDBPDB filePDB Download

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