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

Workflow

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.

PDBConnectorPDB Advanced QueryPDB Custom ReportRCSB PDBPDB filePDB Download
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

Download

Get this workflow from the following link: Download

Resources

Nodes

01_​PDB_​Query_​Download_​and_​Save_​Locally consists of the following 16 nodes(s):

Plugins

01_​PDB_​Query_​Download_​and_​Save_​Locally contains nodes provided by the following 4 plugin(s):