This nodes computes similarities between pairs of molecules by taking the size of their MCSS as a measure
for similarity (the bigger the MCSS the more similar the molecules are). For computing the MCSS, the
substructure miner MoSS is used. Since the computation of a MCSS is a complex problem and can take quite
a lot of time you can set a timeout after which the computation of a single MCSS between two molecule is aborted.
In this case the distance between the two molecules will be the biggest common substructure found so far.
This node may use quite a lot of memory thus if you run into problems try
to increase the available heap size for KNIME in the knime.ini.
Options
Popular Predecessors
- MoSS MCSS Molecule Similarity7 %
- OpenBabel5 %
- RDKit From Molecule5 %
- RDKit Diversity Picker4 %
- Molecule to CDK4 %
- RDKit Fingerprint4 %
- GroupBy3 %
- SDF Reader3 %
CSV Reader3 %- Fingerprint Bayesian Predictor3 %
- Partitioning2 %
- Molecule Type Cast2 %
- MoSS2 %
- Shuffle2 %
- Fingerprints2 %
- Molfile Reader2 %
- Rule-based Row Splitter2 %
- Advanced MolConverter1 %
- Column Filter1 %
Joiner1 %- SDF Extractor1 %
- Distance Matrix Calculate1 %
- TF1 %
- RDKit Optimize Geometry1 %
- Murcko Scaffold1 %
- MarvinSketch1 %
- Substructure Matcher< 1 %
- Uniquify IDs< 1 %
- Fingerprint Similarity< 1 %
File Reader< 1 %Row Filter (deprecated)< 1 %- Reference Row Filter< 1 %
- Row Sampling< 1 %
Excel Reader (XLS)< 1 %- Fingerprint Similarity< 1 %
- MCS Scaffold Finder< 1 %
- Number to String< 1 %
- Column Merger< 1 %
- Smiles Directory Reader< 1 %
- RDKit Find Murcko Scaffolds< 1 %
- RDKit Salt Stripper< 1 %
- MolConverter< 1 %
- Concatenate< 1 %
Column Rename< 1 %- RowID< 1 %
- Rule Engine< 1 %
- SDF Stripper< 1 %
- RDKit Descriptor Calculation< 1 %
- RDKit MCS< 1 %
- RDKit Molecule Fragmenter< 1 %
- RDKit To Molecule< 1 %
- RDKit Two Component Reaction< 1 %
- Speedy SMILES De-salt< 1 %
- Table Creator< 1 %
- Group Loop Start< 1 %
- Hierarchical Clustering< 1 %
- MultiLayerPerceptron Predictor< 1 %
PCA< 1 %- Distance Matrix Pair Extractor< 1 %
Concatenate (Optional in)< 1 %- Cell Splitter< 1 %
- Column Resorter< 1 %
- Create Table Structure< 1 %
- Duplicate Row Filter< 1 %
- Reference Column Filter< 1 %
- Filter Apply< 1 %
Row Splitter (deprecated)< 1 %- Rxn/RD Reader< 1 %
- Fingerprint Bayesian Learner< 1 %
- CDK to Molecule< 1 %
- Connectivity< 1 %
- Lipinski's Rule-of-Five< 1 %
- RDKit Count-Based Fingerprint< 1 %
RDKit Structure Normalizer< 1 %- Fingerprint to Set Bits List< 1 %
- CSV Reader< 1 %
- Table Reader< 1 %
- Similarity Search< 1 %
- 3D Coordinates< 1 %
- RDKit Kekulizer< 1 %
Views
- This node has no views
Workflows
05_Score_Erosion_for_Multi_Objective_OptimizationKNIME Hub- BindingDB_FMCT-Fingerprint+MCSKNIME Hub
- BindingDB_FMCT-MCSKNIME Hub
- DrugRepurposingPipeline_OpenTargetsKNIME Hub
Links
- No links available
Developers
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.