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GUI |
CLI |
Spark experiments
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| Search for novel cores for your molecules |
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| Search for new R-groups based on the chemistry and reagents with up-to-date availability information |
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| Grow a starter molecule into new regions of the active site mapped by another ligand |
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| Join two ligands sitting in the same active site with a linker |
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| Cyclize a molecule by joining two atoms with a linker |
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| Search for a replacement group which will displace a crystallographic water molecule near your ligand |
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| Find result molecules picking protein-ligand interactions not mapped by an existing starter or reference ligand |
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| Grow a starter molecule into inoccupied pockets of the active site |
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Finding bioisosteres
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| Start from a 2D molecule |
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| Start from a 3D conformation |
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| Paste a starter molecule from ChemDraw or other applications |
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| Download a starter molecule directly from the RCSB |
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| Control the allowed elements and hybridization of atoms in all new bonds |
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| Search one database at a time, inspecting results between runs, appending new results to an existing project |
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| Search multiple databases in one process by selecting which databases to search at job initiation |
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| Use field, pharmacophore and docking constraints to ensure specific interactions are maintained |
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| Score results against multiple reference molecules |
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| Score results using alternative similarity metrics |
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| Filter on structure at calculation time using SMARTS patterns or fragments drawn with the molecular editor |
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| Filter result molecules at calculation time according to the desired lipophilicity, polar surface area and flexibility profile |
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| Filter result molecules at calculation time according to the desired size criteria |
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| Import or export customized process settings |
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| Connect to Cresset Engine Broker from Windows, Linux or Mac to use cloud and/or cluster resources for calculations |
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| Use all available CPU resources to speed up calculations |
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Viewing results
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| Browse 2D depictions of result molecules |
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| Get every result molecule in 3D aligned to the starting molecule |
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| View starter and results molecules and the protein in stereo |
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| View protein ribbons in different styles |
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| Limit protein to active site with simple button |
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| View protein ribbons for the active site only |
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| Use the Storyboard to capture, annotate, record and recall scenes from the 3D window |
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| Filter results on structure using SMARTS patterns or fragments drawn with the molecular editor to visualize those which include or exclude the specified fragment |
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| Enable or disable filters using a toggle button |
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| Import or export filters |
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| Cluster results into separate chemotypes based on Murcko scaffolds |
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| Cluster results using skeletons or substitution patterns |
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| View results and associated data in a tiled layout to see multiple structures at a glance |
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Multi-parameter scoring
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| Define a scoring profile that combines bioisosterism and physico-chemical properties |
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| View the physical properties of result molecules in an intuitive radial plot |
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| Assess overall multi-parameter molecule profile using radial plots and colors |
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| Summarize property profile into a single radial plot score |
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| Perform Multi-Parameter Scoring by filtering and ranking molecules according to radial plot score |
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| Ensure that every new idea meets corporate or project guidelines for standard physical properties (e.g. logP, TPSA, MW etc.) |
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| Ensure that conformations for new ideas are realistic by monitoring the torsion frequency in the CSD |
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| Mark specific results as favorites for further investigation |
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| Tag specific results with a custom label for further investigation |
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| Assess chemical feasibility of new ideas by monitoring the attachment point atom type |
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| Import or export custom radial plot properties |
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Database management
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| Create custom databases by fragmenting your corporate database |
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| Control the size and flexibility of fragments that are stored in the database |
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| Convert your available reagents into databases to search today using easily understood yet comprehensive rules |
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| Create your own rules for conversion of reagents into fragment databases to be searched |
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| View which databases need updating before you start a search |
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| Filter by name to easily locate the databases you want to search or update |
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| Update all or select the desired Spark databases in one go |
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Workflow integration
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| Import calculated and/or measured physical properties and data from an external web service through a REST interface |
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| Deploy in a standard workflow in KNIME™ or Pipeline Pilot™ |
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Exporting results
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| Send selected and favorite compounds to Flare™ and Forge™ for further analysis |
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| Export results in standard molecule formats such as sdf or mol2 |
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| Export results as csv for use in Excel, Spotfire etc. (structures are exported as SMILES strings) |
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| Export MEP surfaces as the CCP4, Cube, Insight and MOE file formats |
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