Plugin releases

81

GIS docs, release notes

GIS provides support for displaying geospatial data.

Map viewer

Map viewer displays geospatial data on a map as markers or heatmap.
map-viewer

Custom file viewers

Custom file viewers allow users to view files of various geographic extensions. Supported extensions include:

  • .geojson
  • .topojson
  • .kmz
  • .kml

To view a file, navigate to Browse, locate your data, and click on the file.
map-custom-file-viewer

1 Like
82

Diff Studio 1.3.0 (2025-03-29) docs

This release improves UI/UX:

  • Updated Bioreactor and PK-PD models and demo applications
  • Implemented the Add to Model Hub feature
2 Likes
83

Retrosynthesis 1.0.1 (2025-03-31) docs, release notes

Works backward from a target molecule (the desired final product) to identify simpler, commercially available starting materials and the synthetic reactions needed to reach the target.

To use, click or sketch a molecule, and expand the “Retrosynthesis” context panel on the right:

1 Like
84

CDD Vault Link 1.0.0 (2025-04-01) docs, release notes

Provides integration with CDD Vault registration system. To use the plugin, you must be registered in the CDD Vault system and have at least one vault set up.

To use the application, go to Browse panel > Apps > Chem > CDD Vault. A list of all available vaults is opened under the CDD Vault tab. Each vault contains three tabs:

  • Molecules - the list of all available molecules in the vault. Id column contains links to the corresponding molecules in your vault.
  • Molecules tab
  • Search - basic search through your vault, containing similarity and diversity searches. Search tab
  • Saved searches - open tab to see the list of all saved searches in your vault. Click any search in the list to open the search results.
  • Saved search

There is also a tab in the Context Panel. To use, click or sketch a molecule, and expand the Databases > CDD Vault context tab :
Context panel

1 Like
85

NMRium 1.2.0 (2025-03-29) docs, release notes

NMRium is a file viewer for NMR data, built on top of the awesome NMRium library.

Click on the .jdx file in the browse tree, and the interactive analysis appears in the preview pane.

1 Like
86

Spectra Viewer docs, release notes

Spectra Viewer is a wrapper package for the Datagrok platform using chem-spectra-editor tool. Package allows preview of jdx format for various types of spectra, including IR, UV, Mass, HPLC, absorption and others.

2 Likes
87

BioNeMo docs, release notes

The BioNeMo plugin provides streamlined access to cutting-edge AI models from NVIDIA’s BioNeMo framework, enabling advanced protein structure prediction and molecular docking directly within your workflow.To use BioNeMo, you need an NGC API key for either cloud or local access.

Main features:

  • Protein structure prediction with EsmFold

esmfold

  • Molecular docking with DiffDock

diffdock

  • Works for entire columns or individual molecules
3 Likes
88

Bio 2.20.3 (2025-04-01) docs, release notes

Features:

  • Detectors: more sensitive for very likely column names
  • Added to atomic level panel widget
  • Improved Activity Cliffs demo

Bug fixes:

  • Fixed Sim/Div viewers
2 Likes
89

Hit Triage 1.7.0 (2025-04-01) docs, release notes

Features:

  • Added caching to loaded campaigns
  • Enabled parallel loading of campaigns
  • Implemented lazy loading of function dialogs
  • Enabled compatibility with new Browse version

Bug Fixes:

  • Fixed saving issue for campaigns
  • Fixed URL logic
2 Likes
90

Charts 1.5.1 (2025-04-01): docs, release notes

Features:

  • Moved Multiplot from separate package to Charts

Bug fixes:

  • 3307: Tree viewer not clickable upper node
2 Likes
91

Chem 1.15.0 (2025-03-29) docs, release notes

Features

  • #3273: Scaffold tree: Added the ability to apply scaffold tree colors to scatterplot or other viewers
  • #3314: Scaffold Tree: Demo improvements
  • Scaffold Tree: Implemented the persistence of the previous hide/show state
  • MMP:
    • Added the ability to open the scatter plot context menu when right-clicking on the cliffs scatterplot
    • Implemented separate generation of scatterplots for each activity
    • Improved the Cliffs tab scatterplot
    • Enhanced the trellis plot filters
    • Enabled the use of column descriptions instead of custom tooltips for non-molecule columns
    • Added a help URL
  • Cluster MCL implementation
  • Parallel beautification
2 Likes
92

Curves 1.6.0 - 1.8.0 docs, release notes

The latest versions of Curves bring significant performance improvements and enhanced functionality, including fitting caching, outlier handling, and support for multi-plate files. Key features also include automatic plate import from Excel, improved rendering for 1536-well plates, and integration with new plate readers like Delfia Envision and Spectramax.

Integration with assay plates

For several commonly used formats representing assay plates, Curves automatically detects layout, concentration, and activity layers and shows plate content in the form of automatically fitted dose-response curves.

While typically such functionality gets integrated into custom apps (for instance, for doing the quality control, registering experiments to ELN, etc), this is quite useful for previewing plates. In this picture, excel files are recognized as containing assay plate data, and we can see dose-response curves in the file preview.

Plate readers

The package provides support for some of the common plate formats produced by instruments, such as BMG Pherastar, Delfia Envision, and Spectramax. The detection / parsing mechanism is extensible, so you can easily write your own reader - see examples.

2 Likes
93

Retrosynthesis 1.0.4 (2025-04-07) docs, release notes

  • Removed the Retrosynthesis function from the Top Menu
2 Likes
94

Hit Triage 1.7.2 (2025-04-09) docs, release notes

  • Added the ability to reorder/hide functions in the new template or functions dialog
2 Likes
95

Compute 1.42.2 (2025-04-10) docs

Updated the Parameter optimization feature:

  • Target columns selection
  • Output curves similarity control
  • Improved navigation
2 Likes
96

Diff Studio 1.3.3 (2025-04-10) docs

This release improves parameters optimization:

  • Updated output curves similarity control
  • Implemented target function columns selection
  • Added the navigation panel and the progress indication bar
2 Likes
97

Biostructure Viewer 1.4.1 (2025-04-01) docs, release notes

The Biostructure Viewer plugin enables visualization and interaction with molecular structures and density volumes in Datagrok. It supports Molecule3D semantic types and integrates seamlessly with Datagrok’s grid and file handling system.

Supported Formats

  • Molecular structures: mmCIF, PDB, PQR, GRO, MMTF

  • Density volumes: MRC/MAP/CCP4, DX/DXBIN, CUBE, BRIX/DSN6, XPLOR/CNS

  • Small molecules: MOL2, SDF, MOL (via the Chem package)

Key Features

  • File previews & handlers: Automatically previews and opens supported files using the Biostructure Viewer

File_preview

  • Rendering: Columns with Molecule3D data are rendered with an NGL-based cell renderer. Clicking a cell opens the viewer to explore the structure details

Cell_renderer

  • Viewers: Both biostructure and NGL viewers use the same method to obtain structural data into the viewer from different sources (in order of priority) controlled by properties of the ‘Data’ category:
  1. A PDB string value of the ‘pdb’ property.
  2. A PDB string value of the data frame tag named ‘pdbTag’ property.
  3. A PDB string value of the data frame ‘.pdb’ tag in case the ‘pdbTag’ property is not specified.

NGL_viewer

3 Likes
98

Docking docs, release notes

The Docking plugin integrates the AutoDock GPU, enabling docking simulations of small molecules (ligands) with target macromolecules directly within the Datagrok platform.

Setup Requirements

  • Prepare the target macromolecule: Use AutoDock tools to convert your macromolecule to PDBQT format and create a grid parameter file. Place both files in System:AppData/Docking/targets/<target-name>

  • Prepare ligand data: Load or create a dataframe of ligands. You can also use demo data from System:AppData/Docking/demo_files

Docking workflow

  1. Go to Chem > Docking > Autodock. A dialog appears.

  2. In the dialog:

    • Select the ligands column from your dataframe.

    • Choose a target folder with docking files.

    • Set the number of conformations to explore.

  3. Run the simulation. Initial grid setup may take up to a minute; results are cached for faster reruns.

docking simulations

  1. Analyze results:

  • View docking poses and free energy values.

  • Zoom into binding pockets via the Molstar viewer.

  • Explore calculated properties for deeper analysis.

additional properties

2 Likes
99

Bio 2.21.0 (2025-04-14) docs, release notes

Features:

  • Moved separator refinement to the seq-handler stage
  • Added support for rendering macromolecule differences using custom notation
  • Improved OCL mol converter with non-blocking behavior

Bug fixes:

  • Fixed linearization, wrong R-groups, and notation problems for toAtomicLevel
2 Likes
100

HELM 2.10.0 (2025-04-14) docs, release notes

  • Implemented Non-Drawing HWE for faster pseudo-molfile retrieval
2 Likes