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: |