Forge™ licensing options
Molecule visualization
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Forge Design |
Forge GUI |
Forge CLI |
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| Load protein-ligand crystal structures 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
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Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
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| Calculate low energy conformations for the compounds in the molecules table | ✔ | ✔ | ✔ | ✔ |
| 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 | ✔ | ✔ |
Forge licensing options
Virtual screening
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Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
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| 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 | ✔ | ✔ |
SAR interpretation
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Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
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| 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 | ✔ | |||
| Create detailed 3D-QSAR models for multiple activities | ✔ | ✔ | ||
| Score new molecules against detailed 3D-QSAR models | ✔ | ✔ | ✔ | |
| 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
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Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
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| 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 | ✔ | ✔ | ||
| Design new molecules in common drawing packages and paste into application | ✔ | ✔ | ||
| Use Activity Atlas to calculate a novelty score for new designs | ✔ | ✔ | ✔ | |
| Use k-Nearest Neighbor analysis 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
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Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
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| 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 | ✔ | ✔ | ||
| Sort on any column | ✔ | ✔ | ||
| Duplicate any column | ✔ | ✔ | ||
| Numerical and text filter on any column | ✔ | ✔ | ||
| Add, remove, show and hide columns | ✔ | ✔ | ||
| Color molecule table according to radial plot properties | ✔ | ✔ | ||
| Sort on radial plot to bring compounds with the best properties to the top | ✔ | ✔ | ||
| 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 | ✔ | ✔ |
Workflow integration
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Torch3D |
Forge Design |
Forge GUI |
Forge CLI |
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| KNIME™ integration | As a viewer | As a viewer | ✔ | |
| Pipeline Pilot™ integration | As a viewer | As a viewer | ✔ |