Licensing Spark™
Spark in Flare™ licensing options
| GUI | CLI | |
Interface |
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| Ribbon menu structure for quick identification of commands and controls | ✔ | |
| Customize the display of tabs and function buttons in the ribbon menu using the Flare profiles | ✔ | |
| Launch multiple jobs locally or remotely | ✔ | ✔ |
| Monitor all running, queued, finished and cancelled jobs | ✔ | |
| Summary and detailed logging of calculations and events | ✔ | ✔ |
| Visualize protein-ligand interactions and steric clashes | ✔ | |
| Easily compare protein-ligand complexes | ✔ | |
| Grid the 3D window by protein and ligand to compare and contrast | ✔ | |
| Capture 3D view to the storyboard to track and communicate ideas | ✔ | |
| Create stunning high definition pictures for communication of results | ✔ | |
| Create informative videos of the 3D view and of the Flare GUI | ✔ | |
| Create interactive multi-series scatter plots boxplots and histograms of biological or physical properties | ✔ | |
System (ligand and protein) preparation |
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Dedicated protein table enabling rapid inspection of specific chains or residues |
✔ | |
| Protein sequence alignment and superposition | ✔ | ✔ |
| Control every protein surface with individual display options in the dedicated protein surfaces table | ✔ | |
| Load and view electron density maps | ✔ | |
| Monitor alternate conformations for ligands and protein residues | ✔ | |
| Check protein structures for potential problems | ✔ | ✔ |
| Calculate and color protein molecular surfaces by secondary structure and hydrophobicity | ✔ | ✔ |
| Prepare proteins for further calculation | ✔ | ✔ |
| Perform single point mutation for your proteins | ✔ | ✔ |
| Protein minimization | ✔ | ✔ |
| Dedicated ligand table to store all ligands in your project with full visibility control, sortable on any column | ✔ | |
| Design ligands in the active site of the protein | ✔ | |
| Prepare ligands for further calculation | ✔ | |
| Calculated physico-chemical properties for each ligand | ✔ | ✔ |
| Calculate radial plot multi-parametric scores to select the compounds with the best properties | ✔ | ✔ |
| Filter ligands on physico-chemical properties, structures and tags | ✔ | |
| Visualize ligand electrostatics to gain a deep understanding of SAR | ✔ | |
| Minimize one or more ligands in the protein active site | ✔ | ✔ |
| Perform a geometry check of ligand torsions using the Mogul Library from CCDC (requires a CSD license) | ✔ | |
| Easy and accurate docking of ligands using 1 CPU core including ensemble, template and covalent docking methods | ✔ | ✔ |
| Constrain docking experiments to ensure specific pharmacophoric features are always matched | ✔ | ✔ |
| Dock ligands using multiple CPU cores including ensemble, template and covalent docking methods | Add-on | Add-on |
| Use HPC resources to rapidly dock thousands of ligands | Add-on | Add-on |
Spark experiments |
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| Search for novel cores for your molecules | ✔ | ✔ |
| Search for new R-groups based on the chemistry and reagents with up-to-date availability information | ✔ | ✔ |
| Grow a starter molecule into new regions of the active site mapped by another ligand | ✔ | ✔ |
| Join two ligands sitting in the same active site with a linker | ✔ | ✔ |
| Cyclize a molecule by joining two atoms with a linker | ✔ | ✔ |
| Search for a replacement group which will displace a crystallographic water molecule near your ligand | ✔ | ✔ |
| Find result molecules picking protein-ligand interactions not mapped by an existing starter or reference ligand | ✔ | ✔ |
| Grow a starter molecule into inoccupied pockets of the active site | ✔ | ✔ |
Finding bioisosteres |
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| Start from a 2D molecule | ✔ | ✔ |
| Start from a 3D conformation | ✔ | ✔ |
| Paste a starter molecule from ChemDraw or other applications | ✔ | |
| Download a starter molecule directly from the RCSB | ✔ | |
| Control the allowed elements and hybridization of atoms in all new bonds | ✔ | ✔ |
| Search one database at a time, inspecting results between runs, appending new results to an existing project | ✔ | ✔ |
| Search multiple databases in one process by selecting which databases to search at job initiation | ✔ | ✔ |
| Use field, pharmacophore and docking constraints to ensure specific interactions are maintained | ✔ | |
| Score results against multiple reference molecules | ✔ | ✔ |
| Score results using alternative similarity metrics | ✔ | ✔ |
| Score results by docking score using 1 CPU core | ✔ | ✔ |
| Filter on structure at calculation time using SMARTS patterns or fragments drawn with the molecular editor | ✔ | ✔ |
| Filter result molecules at calculation time according to the desired lipophilicity, polar surface area and flexibility profile | ✔ | ✔ |
| Filter result molecules at calculation time according to the desired size criteria | ✔ | ✔ |
| Import or export customized process settings | ✔ | ✔ |
| Connect to Cresset Engine Broker from Windows, Linux or Mac to use cloud and/or cluster resources for calculations | Add-on | Add-on |
Viewing results |
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| Browse 2D depictions of result molecules | ✔ | |
| Get every result molecule in 3D aligned to the starting molecule | ✔ | ✔ |
| View starter and results molecules and the protein in stereo | ✔ | |
| View protein ribbons in different styles | ✔ | |
| Limit protein to active site with simple button | ✔ | |
| View protein ribbons for the active site only | ✔ | |
| Use the Storyboard to capture, annotate, record and recall scenes from the 3D window | ✔ | |
| Filter results on properties or structure using SMARTS patterns or fragments drawn with the molecular editor to visualize those which include or exclude the specified fragment | ✔ | |
| Enable or disable filters using a toggle button | ✔ | |
| Cluster results into separate chemotypes based on Murcko scaffolds | ✔ | |
| Cluster results using skeletons or substitution patterns | ✔ | |
| View results and associated data in a tiled layout to see multiple structures at a glance | ✔ | |
Multi-parameter scoring |
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| Define a scoring profile that combines bioisosterism and physico-chemical properties | ✔ | |
| View the physical properties of result molecules in an intuitive radial plot | ✔ | |
| Assess overall multi-parameter molecule profile using radial plots and colors | ✔ | |
| Summarize property profile into a single radial plot score | ✔ | |
| Perform Multi-Parameter Scoring by filtering and ranking molecules according to radial plot score | ✔ | |
| Ensure that every new idea meets corporate or project guidelines for standard physical properties (e.g. logP, TPSA, MW etc.) | ✔ | |
| Ensure that conformations for new ideas are realistic by monitoring the torsion frequency in the CSD | ✔ | |
| Mark specific results as favorites for further investigation | ✔ | |
| Tag specific results with a custom label for further investigation | ✔ | |
| Assess chemical feasibility of new ideas by monitoring the attachment point atom type | ✔ | ✔ |
| Import or export custom radial plot properties | ✔ | |
Database management |
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| Create custom databases by fragmenting your corporate database | ✔ | ✔ |
| Control the size and flexibility of fragments that are stored in the database | ✔ | ✔ |
| Convert your available reagents into databases to search today using easily understood yet comprehensive rules | ✔ | ✔ |
| Create your own rules for conversion of reagents into fragment databases to be searched | ✔ | ✔ |
| View which databases need updating before you start a search | ✔ | |
|
Filter by name to easily locate the databases you want to search or update |
✔ | |
| Update all or select the desired Spark databases in one go | ✔ | ✔ |
Workflow integrations |
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| Import your Spark project direclty into Flare to help you prioritize, via a wide portfolio of ideas and methods, the best molecules to make | ✔ | |
|
Import ligands from a csv (structures read in from a SMILES strings) |
✔ | |
| Access the RDKit cheminformatics toolkit | ✔ | |
| Deploy in a standard workflow in KNIME | ✔ | |
| Export results as csv for use in Excel, Spotfire etc. (structures are exported as SMILES strings) | ✔ | |
| Export MEP surfaces as the CCP4, Cube, Insight and MOE file formats | ✔ | |
| Start a Blaze™ virtual screening experiment on millions of compounds from the GUI | ✔ | |
| Browse and retrieve Blaze search results directly, visualizing enrichment plot and statistics for each Blaze refinement level | ✔ | ✔ |
| Create and automate workflows using the Python® API | ✔ | ✔ |
| Upgrade Flare with Python modules for graphing, statistics, Jupyter® Notebook | ✔ | ✔ |
| Expand the functionality of the Flare GUI using Python extensions | ✔ | ✔ |
|
Export Spark search calculations from the GUI and run them with pyFlare |
✔ | |
| Automate and distribute Spark calculations using pyFlare and Cresset released Python scripts and snippets | Add-on | |
Native Spark licensing options
| GUI | CLI | |
|---|---|---|
Spark experiments |
||
| Search for novel cores for your molecules | ✔ | |
| Search for new R-groups based on the chemistry and reagents with up-to-date availability information | ✔ | |
| Grow a starter molecule into new regions of the active site mapped by another ligand | ✔ | ✔ |
| Join two ligands sitting in the same active site with a linker | ✔ | ✔ |
| Cyclize a molecule by joining two atoms with a linker | ✔ | ✔ |
| Search for a replacement group which will displace a crystallographic water molecule near your ligand | ✔ | ✔ |
| Find result molecules picking protein-ligand interactions not mapped by an existing starter or reference ligand | Add-on | Add-on |
| Grow a starter molecule into inoccupied pockets of the active site | Add-on | Add-on |
Finding bioisosteres |
||
| Start from a 2D molecule | ✔ | |
| Start from a 3D conformation | ✔ | ✔ |
| Paste a starter molecule from ChemDraw or other applications | ✔ | |
| Download a starter molecule directly from the RCSB | ✔ | |
| Control the allowed elements and hybridization of atoms in all new bonds | ✔ | ✔ |
| Search one database at a time, inspecting results between runs, appending new results to an existing project | ✔ | |
| Search multiple databases in one process by selecting which databases to search at job initiation | ✔ | ✔ |
| Use field, pharmacophore and docking constraints to ensure specific interactions are maintained | ✔ | ✔ |
| Score results against multiple reference molecules | ✔ | ✔ |
| Score results using alternative similarity metrics | ✔ | ✔ |
| Filter on structure at calculation time using SMARTS patterns or fragments drawn with the molecular editor | ✔ | ✔ |
| Filter result molecules at calculation time according to the desired lipophilicity, polar surface area and flexibility profile | ✔ | ✔ |
| Filter result molecules at calculation time according to the desired size criteria | ✔ | ✔ |
| Import or export customized process settings | ✔ | |
| Connect to Cresset Engine Broker from Windows, Linux or Mac to use cloud and/or cluster resources for calculations | Add-on | Add-on |
| Use all available CPU resources to speed up calculations | Add-on | Add-on |
Viewing results |
||
| Browse 2D depictions of result molecules | ✔ | |
| Get every result molecule in 3D aligned to the starting molecule | ✔ | ✔ |
| View starter and results molecules and the protein in stereo | ✔ | |
| View protein ribbons in different styles | ✔ | |
| Limit protein to active site with simple button | ✔ | |
| View protein ribbons for the active site only | ✔ | |
| Use the Storyboard to capture, annotate, record and recall scenes from the 3D window | ✔ | |
| Filter results on structure using SMARTS patterns or fragments drawn with the molecular editor to visualize those which include or exclude the specified fragment | ✔ | |
| Enable or disable filters using a toggle button | ✔ | |
| Import or export filters | ✔ | |
| Cluster results into separate chemotypes based on Murcko scaffolds | ✔ | |
| Cluster results using skeletons or substitution patterns | ✔ | |
| View results and associated data in a tiled layout to see multiple structures at a glance | ✔ | |
Multi-parameter scoring |
||
| Define a scoring profile that combines bioisosterism and physico-chemical properties | ||
| View the physical properties of result molecules in an intuitive radial plot | ✔ | |
| Assess overall multi-parameter molecule profile using radial plots and colors | ✔ | |
| Summarize property profile into a single radial plot score | ✔ | |
| Perform Multi-Parameter Scoring by filtering and ranking molecules according to radial plot score | ✔ | |
| Ensure that every new idea meets corporate or project guidelines for standard physical properties (e.g. logP, TPSA, MW etc.) | ✔ | |
| Ensure that conformations for new ideas are realistic by monitoring the torsion frequency in the CSD | ✔ | |
| Mark specific results as favorites for further investigation | ✔ | |
| Tag specific results with a custom label for further investigation | ✔ | |
| Assess chemical feasibility of new ideas by monitoring the attachment point atom type | ✔ | ✔ |
| Import or export custom radial plot properties | ✔ | |
Database management |
||
| Create custom databases by fragmenting your corporate database | ✔ | ✔ |
| Control the size and flexibility of fragments that are stored in the database | ✔ | ✔ |
| Convert your available reagents into databases to search today using easily understood yet comprehensive rules | ✔ | ✔ |
| Create your own rules for conversion of reagents into fragment databases to be searched | ✔ | ✔ |
| View which databases need updating before you start a search | ✔ | |
| Filter by name to easily locate the databases you want to search or update | ✔ | |
| Update all or select the desired Spark databases in one go | ✔ | ✔ |
Workflow integration |
||
| Import calculated and/or measured physical properties and data from an external web service through a REST interface | ✔ | |
| Deploy in a standard workflow in KNIME™ or Pipeline Pilot™ | ✔ | |
Exporting results |
||
| Send selected and favorite compounds to Flare™ and Forge™ for further analysis | ✔ | |
| Export results in standard molecule formats such as sdf or mol2 | ✔ | ✔ |
| Export results as csv for use in Excel, Spotfire etc. (structures are exported as SMILES strings) | ✔ | |
| Export MEP surfaces as the CCP4, Cube, Insight and MOE file formats | ✔ | |