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TeachOpenCADD_​Workflow8_​Data_​acquisition_​PDB

Workflow

TeachOpenCADD Workflow 8: Data acquisition from PDB

The PDB database holds 3D structural data and meta information on experimentally resolved proteins.
This workflow shows how structural data can be automatically fetched from the PDB and processed.

PDBWeb service queryData filtering
8. Data acquisition from PDBThe PDB database holds 3D structural data and meta information onexperimentally resolved proteins. The following steps show howstructural data can be automatically fetched from the PDB andprocessed. Step 1Get PDB IDs from UniProt ID of query target Step 2Filter PDB structure: X-ray, resolution <= 3A, and ligand with MW >= 100 present Step 3Keep top 4 protein-ligand structures (sorted by resolution) and download PDB files Change UniProt ID: - Double click on "PDB Connector XML Query Builder" node- Choose "IDs and Keywords" tab- Change UniProt ID in "UniProtKB Accession Number(s)" fieldChoose type of information to be downloaded from PDB:- Double click on "Custom Report" node- Choose "Report Options" tab- Choose type of information for downloadThis workflow adapts the KNIME workflow example 99_Commu-nity/04_Vernalis/01_PDB_Query_Downloder_and_Save_Locally(KNIME EXAMPLES Server, accessed: 2019-05-24) * This step is needed for next node where each PDB ID is filtered for largest, i.e. first, ligand. This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow on our TeachOpenCADD platform: https://github.com/volkamerlab/TeachOpenCADD/blob/master/talktorials/8_PDB/T8_PDB.ipynb Please connect nodes if not connected. Note for "PDB Saver": Please update the output path byclicking on Browse or specify one of your choice (doubleclick "PDB Saver" node to access its configuration menu).Build a query forP00533Query PDBGet structure reportfrom PDBOnly X-raystructuresResolution <= 3.0Only structureswith ligandLigand MW >= 100Keep largestligand onlySave PDB files in resultsBy Ligand MW*By resolutionFilter top 4 structures PDB Connector XMLQuery Builder PDB Connector QueryOnly (XML Query) PDB ConnectorCustom Report Row Filter Numeric RowSplitter Row Filter Row Filter GroupBy PDB Downloader PDB Saver Sorter Sorter Row Filter String Manipulation 8. Data acquisition from PDBThe PDB database holds 3D structural data and meta information onexperimentally resolved proteins. The following steps show howstructural data can be automatically fetched from the PDB andprocessed. Step 1Get PDB IDs from UniProt ID of query target Step 2Filter PDB structure: X-ray, resolution <= 3A, and ligand with MW >= 100 present Step 3Keep top 4 protein-ligand structures (sorted by resolution) and download PDB files Change UniProt ID: - Double click on "PDB Connector XML Query Builder" node- Choose "IDs and Keywords" tab- Change UniProt ID in "UniProtKB Accession Number(s)" fieldChoose type of information to be downloaded from PDB:- Double click on "Custom Report" node- Choose "Report Options" tab- Choose type of information for downloadThis workflow adapts the KNIME workflow example 99_Commu-nity/04_Vernalis/01_PDB_Query_Downloder_and_Save_Locally(KNIME EXAMPLES Server, accessed: 2019-05-24) * This step is needed for next node where each PDB ID is filtered for largest, i.e. first, ligand. This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow on our TeachOpenCADD platform: https://github.com/volkamerlab/TeachOpenCADD/blob/master/talktorials/8_PDB/T8_PDB.ipynb Please connect nodes if not connected. Note for "PDB Saver": Please update the output path byclicking on Browse or specify one of your choice (doubleclick "PDB Saver" node to access its configuration menu).Build a query forP00533Query PDBGet structure reportfrom PDBOnly X-raystructuresResolution <= 3.0Only structureswith ligandLigand MW >= 100Keep largestligand onlySave PDB files in resultsBy Ligand MW*By resolutionFilter top 4 structures PDB Connector XMLQuery Builder PDB Connector QueryOnly (XML Query) PDB ConnectorCustom Report Row Filter Numeric RowSplitter Row Filter Row Filter GroupBy PDB Downloader PDB Saver Sorter Sorter Row Filter String Manipulation

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Nodes

TeachOpenCADD_​Workflow8_​Data_​acquisition_​PDB consists of the following 14 nodes(s):

Plugins

TeachOpenCADD_​Workflow8_​Data_​acquisition_​PDB contains nodes provided by the following 4 plugin(s):