Forge Design |
Forge GUI |
Forge CLI |
||
Load protein-ligand crystal structures from multiple locations to visualize favorable interactions | ✔ | ✔ | ✔ | |
Load up to 10,000 molecules and convert them into 3D so 2D and 3D structures can be viewed side by side | ✔ | ✔ | ✔ | |
Load results of a ligand or protein based virtual screening experiment | ✔ | ✔ | ||
Study SAR of congeneric series by manually modifying structures and visualizing the change in the electrostatic and shape characteristics of the molecules | ✔ | ✔ | ||
View ligands and 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 | ✔ | ✔ | ||
Filter molecules on structure to visualize those which include or exclude the specified sub-structure | ✔ | ✔ | ||
View molecules and associated data in a tiled layout to see multiple structures at a glance | ✔ | ✔ | ||
Use the Storyboard to capture, annotate, record and recall scenes from the 3D window | ✔ | ✔ | ||
Export Cresset field surfaces | ✔ | ✔ | ✔ |
Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
|
Calculate low energy conformations for the compounds in the molecules table | ✔ | ✔ | ✔ | ✔ |
Automatically filter out undesirable conformations during the conformation hunt | ✔ | ✔ | ✔ | |
Inspect conformation populations for the molecules of interest, deleting uninteresting conformations as appropriate | ✔ | |||
Color conformations by conformational energies | ✔ | |||
Calculate distance, angle and torsion monitors for conformations populations | ✔ | |||
Plot energies, distance, angle and torsion monitors for conformations populations | ✔ | |||
Calculate CSD torsion frequencies for the rotatable bonds in a conformation population, based on the Torsion Library method | ✔ | |||
Color rotatable bonds by CSD torsion frequency | ✔ | |||
Filter conformations by energy, monitors and CSD torsion frequencies | ✔ | |||
Understand the binding of diverse ligands by comparing them to a known inhibitor from a protein-ligand crystal structure | ✔ | ✔ | ✔ | ✔ |
Use a protein structure as an excluded volume around ligands in alignment and comparison studies | ✔ | ✔ | ✔ | ✔ |
Constrain molecular comparisons to ensure specific pharmacophoric and field features are always matched | ✔ | ✔ | ✔ | |
Control each step of the experiment with detailed options | ✔ | ✔ | ✔ | |
Score aligned compounds using different similarity metrics | ✔ | ✔ | ||
Use multiple reference ligands to define how ligands bind you to protein | ✔ | ✔ | ✔ | |
Cross compare multiple structures to find a consensus alignment | ✔ | ✔ | ||
Develop detailed models of binding starting in absence of 3D information or protein crystal structures | ✔ | ✔ | ||
Find a pharmacophore that can be used as a template for aligning other active molecule | ✔ | ✔ | ||
Align and compare molecules using a common substructure or using electrostatic and shape characteristics | ✔ | ✔ | ✔ | |
Define the common substructure to align your compounds | ✔ | ✔ | ||
Connect to Cresset Engine Broker from Windows, Linux or Mac to use cloud and/or cluster resources for calculations | ✔ | ✔ | ||
Use all available CPU resources to speed up calculations | ✔ | ✔ | ✔ | |
Import or export customized process settings | ✔ | ✔ |
Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
|
Virtual screening of 500 molecules | ✔ | ✔ | ✔ | ✔ |
Virtual screening of 10,000 molecules | ✔ | ✔ | ||
Virtual screening of 100,000 molecules | ✔ | |||
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 | ✔ | ✔ |
Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
|
Automatically create the most predictive regression models for activity using Machine Learning methods | ✔ | ✔ | ||
Automatically create the most predictive classification models for categorical activity using Machine Learning methods | ✔ | ✔ | ||
Create detailed Field QSAR models for multiple activities | ✔ | ✔ | ||
Score new molecules against Field QSAR and Machine Learning models | ✔ | ✔ | ✔ | |
Spot outliers in the 3D descriptor space using the PCA component plot | ✔ | |||
Visually compare different SAR models by opening multiple model windows | ✔ | ✔ | ||
Use Activity Atlas to calculate and display in 3D activity cliffs summaries, using 3D similarity | ✔ | ✔ | ||
Use Activity Atlas to calculate and display in 3D what the active molecules have in common (using 3D similarity) | ✔ | ✔ | ||
Use Activity Atlas to calculate and display in 3D what regions of the aligned molecules have been fully explored (using 3D similarity) | ✔ | ✔ | ||
Use Activity Atlas to calculate a novelty score for each molecule in the data set (using 3D similarity) | ✔ | ✔ | ||
Export Activity Atlas surfaces for display in other applications | ✔ | ✔ | ||
Use Activity Miner to find and examine activity cliffs in 3D and 2D | Option | ✔ | ✔ | |
Use Activity Miner to find and examine selectivity cliffs using 3D and 2D similarity | Option | ✔ | ✔ | |
Use Activity Miner to find and examine activity cliffs using 2D fingerprints | Option | ✔ | ✔ | |
View hierarchical clustering of your molecules using 2D or 3D similarity | ✔ | |||
Assess overall multi-parameter molecule profile using radial plots and colors | ✔ | ✔ | ✔ | |
Create interactive multi-series scatter plots of biological or physical properties | ✔ | ✔ | ||
Create interactive histograms of biological or physical properties | ✔ | ✔ | ✔ |
Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
|
Clone and edit molecules directly in the protein active site | ✔ | ✔ | ||
Save a copy of your design ideas in the molecule table without leaving the molecule editor | ✔ | ✔ | ||
Gain immediate feedback on new designs using the ‘score while you draw’ feature | ✔ | ✔ | ||
Align all molecule designed in the same editing session as you leave the editor | ✔ | ✔ | ||
Design new molecules in common drawing packages and paste into application | ✔ | ✔ | ||
Use Activity Atlas to calculate a novelty score for new designs | ✔ | ✔ | ✔ | |
Use Field QSAR and Machine Learning models to make robust activity predictions for your new designs | ✔ | ✔ | ✔ | |
Automatically create energetically reasonable conformations for new designs and ensure these can bind to your target | ✔ | ✔ | ✔ | |
Carry out multi-parameter optimization using radial plots and colors | ✔ | ✔ | ||
Gain immediate feedback on distribution of physical properties using radial plots | ✔ | ✔ | ||
Monitor the physicochemical and predicted activity profile for new designs using the radial plot in the molecule editor | ✔ | ✔ |
Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
|
Molecule data table containing calculated physical properties and all data loaded from sdf or csv files | ✔ | ✔ | ||
Import calculated and/or measured physical properties and data from an external web service through a REST interface | ✔ | ✔ | ✔ | |
Automatically recognize activity data and convert into log scale | ✔ | ✔ | ||
Automatically calculate selectivity from primary and secondary activities | ✔ | ✔ | ||
Update table by merging from csv file | ✔ | ✔ | ||
Automatically assign selected molecules to roles, based on their Murcko scaffold | ✔ | ✔ | ||
Sort on any column | ✔ | ✔ | ||
Duplicate any column | ✔ | ✔ | ||
Numerical and text filter on any column | ✔ | ✔ | ||
Enable or disable filters using a toggle button | ✔ | ✔ | ||
Add, remove, show and hide columns | ✔ | ✔ | ||
Choose any user column as the molecule title | ✔ | ✔ | ||
Use any column as a label in the 3D window | ✔ | ✔ | ||
Color molecule table according to radial plot properties | ✔ | ✔ | ||
Sort on radial plot to bring compounds with the best properties to the top | ✔ | ✔ | ||
Import or export radial plot properties | ✔ | ✔ | ||
Remove duplicate compounds from the molecule table | ✔ | ✔ | ||
Send selected and favorite compounds to Flare for further analysis | ✔ | ✔ | ||
Use internal editor to create and export Javascript snippets that operate on the molecule table | ✔ | |||
Calculate new columns from molecule or other data using Javascript | ✔ | |||
Create a profile of scripts to be used on project load | ✔ | ✔ | ||
Drag-and-drop to import and export molecules and proteins on Windows | ✔ | ✔ |
Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
|
KNIME™ integration | As a viewer | As a viewer | ✔ | |
Pipeline Pilot™ integration | As a viewer | As a viewer | ✔ | |
Import and export Forge preferences | ✔ | ✔ |