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00_​bindingsiteexploration

Showcase Study: Exploring Binding Sites in PDB Structures

Thsi is a showcase study on how to explore target protein structures on-the-fly with the KNIME nodes for the ProteinsPlus web server (https://proteins.plus). To use the herein applied and additional tools in your workflows, see the links below.


Known Structures (PDB)

High-Quality Chains (StructureProfiler, PDB)


Predicted Binding Sites (DoGSite3)


Similar Binding Sites (SIENA)


Interactions (PoseEdit) & Activities (ActivityFinder, CDK)

pocket volume>= 75
Rule-based Row Filter
PDBentries
PDB Connector Query Executor
StructureProfiler
descriptors
DoGSite3 - Pockets
UniProtAccession(s)
Table Creator
Table Column to Variable
Prepare Input
PDB Connector Query Builder
flexibilityanalysis
Input - SIENA
relevantchains
Reference Row Filter
Prepare Input
failed tests
Rule-based Row Filter
Relevant Chains
high-qualityPDB entries
Reference Row Filter
Table Column to Variable
Prepare Input
PoseEdit
Fingerprint Similarity
Column Renamer
Column Renamer
GroupBy
residues
DoGSite3 - Residues
known binders
Table Creator
Table Row to Variable
Molecule Type Cast
SIENA
Input - DoGSite3
Fingerprints
ActivityFinder
GroupBy
Fingerprints
GroupBy
pocket volume>= 75
Joiner
ligand-boundsimilar binding sites
Rule-based Row Filter

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: cehrt
Created at: 2022-06-19
On NodePit since: 2025-03-16
Last update: 2026-11-10
Created with KNIME version: v5.2.3

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