GUI | CLI | |
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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 | Add-on | Add-on |
Grow a starter molecule into inoccupied pockets of the active site | Add-on | Add-on |
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 | ✔ | ✔ |
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 |
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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 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 |
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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 integration |
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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 |
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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 | ✔ |