Peptides 1.23.2 (2025-04-14) docs, release notes
- Added support for manually assigning notation providers to tables
2 Likes
Dendrogram docs, release notes
The Dendrogram plugin enables the visualization of phylogenetic trees.
Hierarchical Clustering
A user can embed a dendrogram into a grid. For example, ML > Cluster > Hierarchical Clustering builds the tree based on selected features using the specified distance metric and linkage method. Hover, current row, selection, filtering, and row height are synchronized between the grid and the dendrogram in both directions.
Hierarchical clustering supports numeric, macromolecule, and mixed column types. Distance functions vary by macromolecule type:
- Levenshtein for DNA/RNA/Unknown
- Needleman-Wunsch for sequences
- Hamming for pre-aligned sequences
- Tanimoto distance on Morgan fingerprints for molecules
- Manhattan for numeric columns
Distance matrix computation is parallelized using web workers for high performance. Clustering runs in WebAssembly and supports various linkage methods: ward, average, centroid, complete, single, weighted, and median.
Note: When clustering is applied, the dendrogram enforces its own row order, disabling external sorting. If the user sorts by another column, the tree viewer is hidden, and a message appears. The user can then either restore the dendrogram with its sorting or close it to keep the new sort order.
2 Likes
Diff Studio 1.3.5 (2025-04-22) docs
Improved the parameters optimization feature:
- Curves color scheme
- Target column selection input
2 Likes
Compute 1.43.1 docs
Updated the titting feature:
- Target columns selection
- Analysis results displaying
- Goodness of fit viewers creation
2 Likes
Chem 1.15.1 (2025-04-23) docs, release notes
- #3302: Multiple scaffold trees: Naming/coloring should be saved in projects
2 Likes
EDA 1.4.3 docs
This release introduces quadratic Partial Least Squares (PLS) regression, an enhanced method that incorporates squared terms as additional predictors in the standard PLS framework. By accounting for nonlinear relationships in the data, this approach significantly improves model performance and predictive accuracy for machine learning applications:
2 Likes
Bio 2.21.2 (2025-04-28) docs, release notes
Features:
- Added automatic calculation of missing monomer properties when saving or loading monomer libraries
- Improved formatting for source monomer library names for better readability
- Introduced support for sequence space in custom notation
Bug Fixes:
- Weblogo:
- Corrected logo fitting
- Resolved issues with slider interaction
- Harmonized property handling
2 Likes
File Editors docs, release notes
The File Editors plugin enables users to open and preview PDF and DOCX file formats directly within Datagrok
2 Likes
Arrow docs, release notes
The Arrow plugin adds native support for Parquet and Feather file formats in Datagrok.
It is based on the following open-source libraries:
Features:
- File Exporters: Export tables to Parquet and Feather formats
- File Handlers: Open and work with Parquet and Feather files directly in Datagrok
1 Like
SQLite docs, release notes
The SQLite plugin allows users to import and preview SQLite database files directly within Datagrok.
1 Like
DrugBank docs, release notes
The DrugBank plugin enables searching within the DrugBank Open Structures dataset.
Features:
- Substructure Search finds DrugBank structures for the specified substructure
- Similarity Search finds similar DrugBank structures for the specified structure
1 Like
PubChem docs, release notes
The PubChem plugin for Datagrok enables searching in the PubChem database.
Note: Searches are performed externally; the input structure is sent to PubChem as a query parameter.
Features:
- Identity Search finds structures identical to the input, based on various chemical identity criteria.
- Substructure Search finds structures containing the specified substructure.
- Similarity Search finds structures similar to the input structure.
1 Like
Diff Studio 1.3.6 docs
This release implements parallel sensitivity analysis:
3 Likes
Charts 1.5.2 (2025-05-12): docs, release notes
Features
- 3298: Tree:
- Added Ctrl+Click support for branch selection to enable filtering
- Implemented collaborative filtering
Bug Fixes
- GROK-18009: Charts | Sunburst: Errors after changing table with opened ‘Select columns’ dialog
- GROK-18010: Charts | Sunburst: Viewer formatting reset on property changes
- GROK-18011: Charts | Sunburst: Molecules appear smaller/bigger than expected
- GROK-18035: Charts | Sankey: Errors on hover after applying filters
- GROK-18036: Charts | Sankey: Selecting an empty column in the context panel causes errors
- GROK-18085: Charts | Radar: Empty chart after restoring from project
- GROK-18087: Charts | Tree viewer: Size aggregation types ‘nulls’ and ‘#selected’ break the viewer
3 Likes
Bio 2.21.7 (2025-05-14) docs, release notes
Features:
- Added a scrollable header showing sequence positions
- Enable Header scrolling for non-MSA
- Implemented support for shifted sequence rendering
- Implemented support for monomer rendering in viewers
Bug Fixes:
- Similarity search viewer: Fix for clearing selection
- Substructure filter: Corrected event management for setting separator
2 Likes
Peptides 1.23.10 (2025-05-15) docs, release notes
- Improved performance of Peptide viewers
- Reduced white space in the LST
- Added a position statistics viewer
- Improved description for position statistics viewer
2 Likes
Chemspace docs, release notes
The Chemspace plugin integrates Datagrok with the Chemspace, an online store for chemical building blocks.
To start, set your Chemspace apiKey in the package credentials manager.
You can use the pugin in two modes:
-
Application: Sketch a structure in the Toolbox to search Chemspace. The results appear in a table and can be filtered using Toolbox controls.
-
Info Panel: Shows similar, and substructure matches from Chemspace for the selected molecule (Context Panel > Databases > Chemspace).
Note: Structures are sent to Chemspace as query parameters.
Click a result in the Chemspace panel to view it on chem-space.com.
2 Likes
Reinvent4 docs, release notes
The Reinvent4 plugin integrates the REINVENT molecular design tool into Datagrok. Use it for de novo design, scaffold hopping, R-group replacement, linker design, and molecule optimization.
Configuration
The plugin provides several built-in configuration files.
To use a custom configuration:
- Follow the official REINVENT4 setup instructions.
- Place the configuration files in a folder under
System:AppData/Reinvent4/reinvent/<folder-name>. - The folder name will appear as a selectable configuration in the plugin UI.
Generate molecules
- Go to Chem > Generate molecules…
- In the dialog, configure the following parameters:
- Ligand seed: The starting point for ligand generation
- Optimize: The optimization criteria (folder where all configuration files will be stored)
- Click Run to start generation.
3 Likes
Charts 1.5.4 (2025-05-29): docs, release notes
Bug Fixes:
- Sunburst: Limited number of rendered columns
- 3377: Sunburst: Tooltip displays wrong number of rows
3 Likes
Retrosynthesis 1.0.5 (2025-05-29) docs, release notes
- Enabled adding results to the workspace
- Added the ability to use user specific configuration
4 Likes