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TeachOpenCADD_​Workflow8_​Data_​acquisition_​PDB

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.

Step 3Keep top 4 protein-ligand structures (sorted by resolution) and download PDB files 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://projects.volkamerlab.org/teachopencadd/talktorials/T008_query_pdb.html 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, filtered by X-ray, resolution <= 3A, and ligand with MW >= 100 present 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). Step 2Get each structure's resolution & bound ligand ID(s) and MW(s), keep only largest ligand per structure and sort structures by resolution Change UniProt ID: Double click on "PDB Connector Query Builder" node to change theUniProt ID and/or other selection criteriaChoose type of information to be downloaded from PDB:Double click on first "Column Expression" node in Step 2 and buildGraphQL query string of interested following the PDB documentation(https://www.rcsb.org/pages/webservices).Note:Steps 1 and 2 have changed w.r.t. to the originally published workflowdue to changed PDB nodes (due to a changed RCSB PDB API). * This step is needed for next node where each PDB ID is filtered for largest, i.e. first, ligand.Ligand MW >= 100Keep largestligand onlySave PDB files in resultsBy Ligand MW*By resolutionFilter top 4 structuresBuild query for P00533, only X-ray, resolution<=3, has ligand with MW>=100Query PDB for PDB IDs that match conditionsAdd GraphQL query strings Get requested PDB data in json formatAdd PDB URL using GraphQL query stringsConvert datafrom json to table Row Filter GroupBy PDB Downloader PDB Saver Sorter Sorter Row Filter String Manipulation PDB ConnectorQuery Builder PDB ConnectorQuery Executor Column Expressions GET Request Column Expressions Process JSON Step 3Keep top 4 protein-ligand structures (sorted by resolution) and download PDB files 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://projects.volkamerlab.org/teachopencadd/talktorials/T008_query_pdb.html 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, filtered by X-ray, resolution <= 3A, and ligand with MW >= 100 present 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). Step 2Get each structure's resolution & bound ligand ID(s) and MW(s), keep only largest ligand per structure and sort structures by resolution Change UniProt ID: Double click on "PDB Connector Query Builder" node to change theUniProt ID and/or other selection criteriaChoose type of information to be downloaded from PDB:Double click on first "Column Expression" node in Step 2 and buildGraphQL query string of interested following the PDB documentation(https://www.rcsb.org/pages/webservices).Note:Steps 1 and 2 have changed w.r.t. to the originally published workflowdue to changed PDB nodes (due to a changed RCSB PDB API). * This step is needed for next node where each PDB ID is filtered for largest, i.e. first, ligand.Ligand MW >= 100Keep largestligand onlySave PDB files in resultsBy Ligand MW*By resolutionFilter top 4 structuresBuild query for P00533, only X-ray, resolution<=3, has ligand with MW>=100Query PDB for PDB IDs that match conditionsAdd GraphQL query strings Get requested PDB data in json formatAdd PDB URL using GraphQL query stringsConvert datafrom json to tableRow Filter GroupBy PDB Downloader PDB Saver Sorter Sorter Row Filter String Manipulation PDB ConnectorQuery Builder PDB ConnectorQuery Executor Column Expressions GET Request Column Expressions Process JSON

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