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

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 and pharmacophore 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
Connect to remote resources using Cresset Engine Broker

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  
Cluster results into separate chemotypes based on Murcko scaffolds  
Cluster results using skeletons or substitution patterns  

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  
Carry out 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  ✔

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
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  ✔