KNIME node to retrieve (a part of) a kinase-ligand complex as a 3D structure in MOL2/PDB format from KLIFS. This node retrieves a set of MOL2/PDB structures from KLIFS based on a user-supplied set of Structure IDs (based on output from the Structures Overview Retriever node). The user can indicate whether to retrieve the full complex, the protein, the pocket, or the ligand. As output the nodes provides a table of structures based on the KLIFS alignment in MOL2/PDB format with the structure ID. As (all structures retrieved from KLIFS are aligned based on the KLIFS pocket definition this node can, for example, be used to compare ligand binding modes, compare protein structures, or to generate structure-based or ligand-based pharmacophores.
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Advanced Options
Popular Predecessors
- GroupBy14 %
- Column Filter12 %
Row Filter (deprecated)12 %- Structures Overview Retriever9 %
- Chunk Loop Start9 %
- Kinase Information Retriever5 %
- Structures PDB Mapper5 %
- Substructure Search5 %
- Kinase ID Mapper3 %
Python Script (1⇒1)3 %File Reader3 %- HiLite Table (legacy)3 %
- Table Creator2 %
- Column Auto Type Cast2 %
- Reference Row Filter2 %
Column Rename2 %- Structures Retriever2 %
- HiLite Row Splitter2 %
Joiner2 %- PDB Loader2 %
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