Cell Directory

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: