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Molecule visualization

Torch3D

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 ✔ ✔ ✔

Molecular alignment

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 ✔ ✔

Forge licensing options

Virtual screening

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  ✔ ✔

SAR interpretation

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 ✔ ✔ ✔

Designing new molecules

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 ✔ ✔

Molecule table/spreadsheet

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 ✔ ✔

Workflow integration

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 ✔ ✔

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