Directory of cells available in Squonk. You can filter by any of the terms in the table.
Further information about usage is available from page describing the cell.
Entries
Page name | Category | Source | Description |
---|---|---|---|
3DMol.js | Visual | Academic Open Source | Structure 3D viewer, allowing proteins and ligands to be displayed and manipulated. Uses 3DMol.js from University of Pittsburgh |
Abbvie MPS | Molecular Properties | ChemAxon | Multi-Parameter Scoring as defined by Abbvie. |
Atom Count (CXN) | Molecular Properties | ChemAxon | Atom count calculator for structures using ChemAxon's property calculators |
BBB Gupta | Molecular Properties | ChemAxon | Multi-Parameter Scoring of Blood-Brain Barrier permeation. |
Box Plot | Visual | Squonk | Displays data as a box plot using the D3 Javascript library |
CNS MPO (CXN) | Molecular Properties | ChemAxon | Multi-Parameter Optimisation score for drugs targeted at the Central Nervous Systmem (CNS). |
CSV Upload | Input/Output | Squonk | Allows a text file to be uploaded into the system. Comma and tab separated formats are supported along with basic options like whether to handle first line as headers. |
Canonical Smiles (RDKit) | Molecular Properties | RDKit | Generate a canonical smiles string for structures using RDKit |
ChEMBL Activities Fetcher | Input/Output | EBI | Pulls compound and activity data for a specified assay ID from the ChEMBL REST web services at the EBI |
Chemcentral Similarity Search | Structure search | RDKit | Search our "house" databases using similarity search |
Chemcentral Structure Search | Structure search | RDKit | Search our "house" databases using exact or substructure search |
Chemcentral multi-search | Structure search | RDKit | Search our "house" databases to find structures similar to any of the input structures |
Convert to Molecules | Transform | Squonk | Generate molecules from text representation e.g. a smiles column from a CSV file |
Dataset Docker Processor | Programming | Squonk | Process a dataset using a specified Docker container |
Dataset Enricher | Transform | Squonk | Enriches one dataset with content from another |
Dataset Potion | Transform | Squonk | A simple language for performing powerful data transformations |
Dataset UUID filter | Filter | Squonk | Filter a dataset with a set of UUIDs |
Dataset Field Filter | Filter | Squonk | Remove unwanted fields from a dataset. |
Dataset Random Selector | Filter | Squonk | Select records at random from a dataset |
Dataset slice selector | Filter | Squonk | Simple cell that let's you prepare a subset of a large dataset starting at a specified entry and including a specified number of entry |
Dataset sorter | Transform | Squonk | Sort a dataset by one or more fields |
Dataset Split | Transform | Squonk | Split a dataset into 2 datasets according to the number of rows or the fraction of rows. |
Dataset Split using Expression | Transform | Squonk | Split a dataset into 2 datasets according by evaluating a simple expression for a field's values. |
Dataset Split on Null | Transform | Squonk | Split a dataset into 2 datasets according to whether a field has a value. |
Drug-like Filter (CXN) | Molecular Properties | ChemAxon | Apply a drug likeness filter to molecules using ChemAxon's property calculators |
ECFP4 Screen (CXN) | Molecular Screening | ChemAxon | Filter molecules with ECFP fingerprints similarity using ChemAxon's Screen |
Enumerate charges | Transform | Durant Lab | |
Formal Charge (RDKit) | Molecular Properties | RDKit | Calculates the formal charge of a molecule. e.g. 1+, 2+, 1-, 0 (for neutral) |
Frac sp3 C (RDKit) | Molecular Properties | RDKit | Calculate the fraction of sp3 hybridised carbon atoms for structures using RDKit |
Ghose filter (CXN) | Molecular Properties | ChemAxon | Ghose drug like filter implemented with ChemAxon's property calculators |
Ghose filter (RDKit) | Molecular Properties | RDKit | Ghose drug like filter implemented using RDKit |
Groovy Dataset Filter | Filter | Squonk | Filter a dataset based on an expression using the Groovy programming language. |
HBA & HBD (CDK) | Molecular Properties | CDK | H-bond acceptors and donors using Chemistry Development Kit |
HBA & HBD (RDKit) | Molecular Properties | RDKit | Calculate the number of h-bond donors and acceptors for structures using RDKit |
Heatmap | Visual | Squonk | Display of relationships between data using a heatmap |
Image Viewer | Visual | Squonk | Simple viewer for image files |
KiDS MPO (CXN) | Molecular Properties | ChemAxon | Multi-Parameter Optimisation score for kinase drugs. |
Lipinski filter (CXN) | Molecular Properties | ChemAxon | Lipinski filter for structures using ChemAxon's property calculators |
Lipinski filter (RDKit) | Molecular Properties | RDKit | Calculate Lipinski properties for structures using RDKit |
LogD (CXN) | Molecular Properties | ChemAxon | LogD predictor for structures using ChemAxon's property calculators |
LogP (CDK) | Molecular Properties | CDK | ALogP and XLogP predictors for structures using Chemistry Development Kit |
LogP (CXN) | Molecular Properties | ChemAxon | LogP predictor for structures using ChemAxon's property calculators |
LogP (OpenChemLib) | Molecular Properties | OpenChemLib | LogP predictor for structures using OpenChemLib |
LogP (RDKit) | Molecular Properties | RDKit | Predict LogP using RDKit |
LogS (CXN) | Molecular Properties | ChemAxon | LogS (solubility) predictor for structures using ChemAxon's property calculators |
LogS (OpenChemLib) | Molecular Properties | OpenChemLib | Solubility (LogS) predictor for structures using OpenChemLib |
Merge Datasets | Transform | Squonk | Merge multiple datasets into one using a common key. Useful for combining data from multiple sources into a single dataset where there is a common identifier linking the records |
MolAlignAssemblies | Molecular Screening | Other | Alignment of 3D structures |
Molar Refractivity (RDKit) | Molecular Properties | RDKit | Predict molar refractivity using RDKit |
Molecule standardisers | Transform | RDKit | Two cells performing molecular standardisation using the MolVS and Flatkinson standardisers. |
MoleculeEnumerator | Transform | RDKit | Enumerates potential variants of a structure using RDKit |
Molecules From Field | Input/Output | Squonk | Creates a new dataset containing molecules present in the specified field of the input. |
Molfile Upload | Input/Output | Squonk | Allows a dataset to be created from a file in molfile format. The dataset will contain a single structure. |
NGL Viewer | Visual | PDB/RCSB | NGL 3D viewer from Alexander Rose |
PAINS filter (RDKit) | Molecular Properties | RDKit | Filter molecules using PAINS (Pan Assay Interference Compounds) filters, implemented with RDKit |
PDB Upload | Input/Output | Squonk | Allows file in PDB format to be uploaded |
PLI score | 3D | Commercial Open Source | Scores docked structures using the Astex PLI scoring algorithm. |
PSA (OpenChemLib) | Molecular Properties | OpenChemLib | Calculate the polar surface area for structures using OpenChemLib |
Parallel Coordinate Plot | Visual | Squonk | Display and filter data using a parallel coordinate plot |
Pharmacophore Screen (CXN) | Molecular Screening | ChemAxon | Filter molecules with a 2D pharmacophore similarity using ChemAxon's Screen |
RDKit Butina Clustering | Clustering | RDKit | Cluster molecules using the Butina algorithm from RDKit. |
RDKit Cluster Matrix | Clustering | RDKit | Generates a clustered distance matrix from a dataset of molecules using Butina clustering from RDKit. |
RDKit Conformers | Molecular Properties | RDKit | Generate 3D conformers of molecules using RDKit |
RDKit Constrained Conformers | Molecular Properties | RDKit | Generate conformers of a molecule, constraining a part of a molecule to fixed coordinates. |
RDKit Diverse Subset Picker | Clustering | RDKit | Cluster molecules using the Butina algorithm from RDKit and then pick a diverse subset of the molecules |
RDKit MaxMin Picker | Clustering | RDKit | Picks diverse subset of compounds using the MaxMinPicker algorithm as implemented in RDKit |
RDKit Multi-Similarity Screening | Molecular Screening | RDKit | Virtual screening using molecular similarity |
RDKit Open3D Align | Molecular Screening | RDKit | Performs 3D alignment of molecules using Open3DAlign |
RDKit Similarity Screening | Molecular Screening | RDKit | Virtual screening using molecular similarity |
REOS Filter (RDKit) | Molecular Properties | RDKit | Rapid Elimination Of Swill filter - a drug-like structure filter using RDKit |
REOS filter (CXN) | Molecular Properties | ChemAxon | Rapid Elimination Of Swill filter - a drug-like structure filter using ChemAxon |
Ring Count (RDKit) | Molecular Properties | RDKit | Calculate the number of rings and aromatic rings for structures using RDKit |
Rotatable bonds (RDKit) | Molecular Properties | RDKit | Calculate the number of rotatable rings for structures using RDKit |
Rule of 3 filter (CXN) | Molecular Properties | ChemAxon | Astex rule of 3 filter for filtering fragment libraries implemented with ChemAxon |
Rule of 3 filter (RDKit) | Molecular Properties | RDKit | Astex rule of 3 filter for filtering fragment libraries implemented with RDKit |
SDF Export (CDK) | Input/Output | CDK | Export structures to SDF using Chemistry Development Kit |
SDF Upload | Input/Output | Squonk | Allows a MDL SD file to be uploaded into the system. Structures and data are handled. |
SMARTCyp | Molecular Properties | Academic Open Source | SMARTCyp metabolic site prediction |
SMoG2016 | 3D | Academic Open Source | Scores docked structures using the SMoG 2016 scoring algorithm. |
Scatter Plot | Visual | Squonk | Displays data as a scatter plot using the D3 Javascript library |
Simple Sorter | Transform | Squonk | Sort dataset using a single field's value |
Smiles Structures | Input/Output | Squonk | Read structures from smiles strings |
Smiles deduplicator | Filter | Squonk | De-duplicate a set of structures using a canonical smiles field |
SphereEx Clustering (CXN) | Clustering | ChemAxon | Cluster molecules using sphere exclusion clustering and ECFP fingerprints using ChemAxon's JKulstor |
TPSA (RDKit) | Molecular Properties | RDKit | Calculate topological polar surface area for structures using RDKit |
Table Display | Visual | Squonk | Displays data as a familiar table/spreadsheet |
Tmax Cmax Simulation | DMPK | Other | Simulator for Pharmacokinetic profiling of a compound |
Transform Values | Transform | Squonk | Convert data types e.g. convert from text to numbers |
Trusted Groovy Script | Programming | Squonk | Process a dataset using a Groovy script. The script is trusted and executed "in process" |
Untrusted Groovy Script | Programming | Squonk | Process a dataset using a Groovy script. The script is not trusted and executed in its own safe sandbox. |
Veber filter (CXN) | Molecular Properties | ChemAxon | Veber filter for orally active drugs implemented using ChemAxon |
Veber filter (RDKit) | Molecular Properties | RDKit | Veber filter for orally active drugs implemented using RDKit |
Verify structure (CDK) | Input/Output | CDK | Verify that the molecules are valid according to CDK |
Verify structure (CXN) | Input/Output | ChemAxon | Verify that the molecules are valid according to ChemAxon's Marvin |
Verify structure (OCL) | Input/Output | OpenChemLib | Verify that the molecules are valid according to OpenChemLib |
Verify structure (RDKit) | Input/Output | RDKit | Verify that the molecules are valid according to RDKit |
Wiener Numbers (CDK) | Molecular Properties | CDK | Wiener path and polarity numbers using Chemistry Development Kit |
XChem Reaction Maker | Transform | RDKit | Enumerate input molecules using a specified reaction and some reactions |
XChem Reaction Smarts Filter | Molecular Screening | RDKit | Filter a set of molecules according to whether they contain a substructure fragment compatible with a set of reaction types |
ZipFileUpload | Input/Output | Squonk | Cell that allows a zip file to be uploaded. |
pKa (CXN) | Molecular Properties | ChemAxon | Acidic and basic pKa predictors using ChemAxon's property calculators |
rDock Docking | 3D | Commercial Open Source | Ligand docking using rDock. There are two versions of rDock docking: |