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StarDrop™ release notes

Version 7.5 release notes (September 2023)

New Features

Metabolism – Replaces p450:

  • New WhichEnzyme™ model to calculate the relative likelihood of a structure being a substrate of cytochrome P450 (P450), aldehyde oxidase (AOX), flavin-containing monooxygenase (FMO), uridine diphosphate glucuronosyltransferase (UGT) or sulfotransferase (SULT).
  • New Phase I and Phase II enzyme regioselectivity models for AOX1, FMO1/FMO3, UGT1A1/UGT1A4/UGT1A9/UGT2B7 and SULT.
  • New pre-clinical models (mouse/rat/dog) that predict the importance of each potential site of P450 metabolism in animal models.
  • The P450 area in StarDrop has been replaced with a new, streamlined Metabolism area with easy-to-access calculation modes:
    • Predict Metabolism – predicts one generation of metabolism for all enzyme models.
    • Predict P450 Metabolism – predicts one generation of metabolism for all P450 models.
    • Generate Metabolic Pathway – predicts a 2-generation metabolic pathway based on a structure. A heuristics-based model determines which first-generation metabolites are progressed to further metabolism prediction.
    • Custom – the user can decide which models to run.

Surflex eSim3D™ – Desktop Virtual Screening:

  • From the 3D tab, StarDrop users can now run fast, ligand-based virtual screening against prepared screening libraries.
  • Commercially available screening collections from Enamine and MolPort™ have been prepared for virtual screening (conformations pre-computed) and are available for download for use in desktop virtual screening. The screening libraries will be regularly updated.

Core Application:

  • Added the ability to edit and replace/overwrite the chemical structure in a data set row.
  • The 2D chemical diagram in the data set can now be set to a preferred orientation.
  • Added a context menu option to copy a structure from a data set to the clipboard within Table View and Card View®.
  • Added the ability to zoom the display in Table View using the mouse wheel with a CTRL-key modifier (CMD-key on Mac).
  • Added context menu options to Table View column headers and row numbers to set column widths and row heights.
  • Added the ability to select a compound in Card View and then automatically expand the selection to include all compounds linked to the selected card.
  • Added the ability to clean Card View (remove links, annotations, snap to grid, etc.) with a single action.
  • Added a property search bar to the Function Editor dialogue to make it easy to locate columns.

Visualisation:

  • Added an option in the Visualisation Preferences to toggle the selection colour applied to selected/unselected chart data.

SeeSAR™ View:

  • Added the ability for users to reset to a standard orientation in the SeeSAR display.
  • The camera orientation in the SeeSAR display is now saved in the StarDrop project file.
  • Added the ability to export protein-ligand complexes from SeeSAR to a single PDB file.

Nova™:

  • Added the ability to sketch or edit a transformation directly in the Nova Transformation Manager panel.

Changes

Core Application:

  • 2D chemical diagrams in the data set can now be aligned based on structure/substructure, including wildcard matching in a new Align 2D Diagrams tool under the Data Set menu.
  • The label layout for 2D chemical diagrams has been updated to avoid overlapping labels, lines crossing structures, and improving readability.
  • Implicit Hydrogens without 2D coordinates are now shown in grey in the chemical diagram.
  • The size of frozen rows/columns in Table View is now limited so that the main table is always visible.
  • When editing a text cell, the dialogue box is now multi-line with wrapped text.
  • Data set tab order in the Tabbed View and the Cascade View layout are now saved in the StarDrop project file.
  • Improved user preferences interface to control font type, size, and colour in summaries and charts.
  • Improvements have been made to logging preferences, including making it easy to copy the path to the log file and adding the option for StarDrop to write detailed messages to the log.
  • Memory performance has been improved by limiting the undo stack to the most recent 40 actions.
  • PythonQt has been replaced, meaning previously installed StarDrop scripts must be upgraded. A Python Script upgrader has been built to ensure scripts are upgraded when first run.

Nova:

  • Reinstated saving of the Matched Molecular Pair results table to the StarDrop project file so that the analysis does not need to be repeated when the file is reopened.
  • Added the option to include ring changes in fused rings as a matched pair.

Servers:

  • In addition to CentOS, Ubuntu installers are now available for all StarDrop servers.

Bug Fixes

Core Application:

  • Fixed an issue where a new file path to a folder of models set in the File Locations area of the Preferences caused StarDrop to crash.
  • Fixed an issue where StarDrop failed to start after users added a new file path in the File Locations area of the Preferences to access shared custom models (e.g. *.aim files from Auto-Modeller).
  • Fixed an issue where column headers that contained special characters (e.g. /) were not imported from *.csv files.
  • Fixed an issue where users could not select a new heat map colouring scheme on macOS.
  • Fixed an issue where heteroatoms in structures displayed on cards with coloured backgrounds were hard to read.
  • Fixed an issue where heat map colouring was lost in Card View® if the user clicked on white space between cards.
  • Fixed an issue where Card View performance was decreased whilst removing links between selected cards.
  • Fixed an issue where applying the undo action in the Nova layout in Card View caused a crash.
  • Fixed an issue where hovering the cursor over a card in Card View resulted in pixelation on Windows with >150% scaling.
  • Fixed an issue with multi-scaffold R-group decomposition where only the first scaffold was recognised for subsequent enumeration.

Visualisation:

  • Fixed an issue where applying a numerical filter to a scatter plot resulted in the unintended exclusion of compounds.
  • Fixed an issue where radar plots appeared pixelated on Windows with >150% scaling.
  • Fixed an issue where scatter plots were not automatically updating when categorical data was changed.
  • Fixed an issue where column headers that contained special characters (e.g. /) were unavailable for formatting in a visualisation.

Metabolism – Formerly P450:

  • Fixed an issue where P450 metabolites were not generated for some sites that were predicted to be labile.
  • Fixed an issue where the orientation of a molecule in the P450 summary area was inconsistent with its orientation in Table View.

Nova:

  • Fixed an issue where R-group enumeration on a molecule with many R-groups caused a crash.
  • Fixed an issue where a chemistry transformation in Nova resulted in an incorrect chemical structure.
  • Fixed an issue in multi-scaffold R-group analysis where View Scaffold only showed the first scaffold available.

Surflex eSim3D:

  • Fixed an issue where the eSim3D prepared reference structure was not used in the calculation of eSim3D surfaces.
  • Fixed an issue where the C-N bond order in the pyrrolidone moiety of staurosporine-like ligands (PDB HET IDs: STU, 4ST, 1ST, and ITQ) was assigned incorrectly.

Model Server/Auto-Modeller™:

  • Fixed an issue where model metadata in *.aim files encoded in Latin-1 were not read.
  • Fixed an issue where the REST service to Model Server failed when accessed from multiple clients or processes.

Version 7.4 release notes (March 2023)

New Features

Core Application​:

  • Added the ability to colour StarDrop data sets based on property values​ (“Heat Map”)
  • Added the ability to specify the size and position of structure in chart pop-ups
  • Added the ability to specify default properties to be displayed in chart pop-ups
  • Added the ability to synchronise the display of chart pop-ups and labels
  • Added the ability to convert chart pop-ups into labels
  • Added the ability to show chart pop-ups whenever compounds are selected

Scripting:

  • Added the ability to edit data set entries from a script
  • Added the ability to refresh a data set from a script

Query Interface:

  • Added the ability to query on pre-defined SMARTS and TEXT values
  • Added support for categorical data types

Changes

Core Application​:

  • Enhanced behaviour in charts to retain colour formatting of selected data (dimming unselected data points)
  • Histograms now automatically update when a categorical value is changed
  • Tooltips associated with numerical and categorical data now display standard deviations and probabilities respectively
  • Added the ability to export only the best pose when saving a data set that has 3D conformations
    Card View display performance has been improved when loading and clustering larger (100k compounds) data sets
  • Selection tool now only provides Maximin as the diversity metric
  • Molecule View has been removed
  • GLC-lib has been replaced by Qt3D for improved graphics in 3D charts

Nova:

  • Improved Nova transformation rendering now avoids chemical diagrams where all atoms are red
  • Matched series analysis wizard now automatically ticks the first knowledgebase entry only

SeeSAR:

  • Updated to the latest BioSolveIT library

Scripting: 

  • StarDrop now automatically adds a ‘site-packages’ folder to sys.path on startup, which assists the deployment of complex custom scripts
  • Pose Generation Interface now supports Python 3.10
  • Hypertext links and selectable text in warning dialogues are now supported

Servers:

  • Model server extensions can now be customised to specify an error message when calculations fail

Bug Fixes:

Core Application:

  • Fixed an issue where SD files generated by third-party software would not open correctly
  • Fixed an issue where selecting data points on a 3D chart was difficult on a high-resolution screen
  • Fixed an issue where certain 3D scatter plots required higher memory consumption
  • Fixed an issue where snake plot labels for selected items were created incorrectly
  • Fixed an issue where minor tick marks for 3D charts were not available
  • Fixed an issue where points and error bars didn’t line up on jittered and zoomed 3D charts
  • Fixed an issue where text rendering was unreadable due to rendering artefacts in 3D charts on macOS
  • Fixed an issue where the selection tool stalled when running large numbers of rapid iterations for a diverse selection

Nova:

  • Fixed an issue where “Add to Fragment Library” and “Assign to Plate” options were greyed out in the ‘Data Set’ menu on macOS
  • Fixed an issue where macrocycle templates were not being used in the Nova sketcher or when displaying reagents
  • Fixed an issue where incorrect models were available in the list of properties

Servers:

  • Fixed an issue that stopped licenses for the Model Server REST interface working due to time zone differences
  • Fixed an issue that occasionally caused an Auto-Modeller worker process to crash
  • Fixed an issue where StarDrop became periodically unresponsive when the Derek Nexus Server and License Server were configured but both unreachable
  • Fixed an issue where an error message was repeated, resulting in large log files

Scripting: 

  • Fixed an issue in a third-party integration script where an empty string was returned for certain data types
  • Fixed an issue where Python models loaded into StarDrop from a file location were not available without an ADME QSAR license

 

Version 7.3.2 release notes (October 2022)

Bug Fixes

macOS:

  • Fixed an issue where the bundled Python was dependent on system Python libraries
  • Fixed an issue where pyodbc was unable to obtain ODBC driver details
  • Fixed an issue where StarDrop crashed when working with invalid dates

Servers:

  • Fixed an issue where the model server failed to load models when models generated by the Auto-Modeller were present

Version 7.3.1 release notes (July 2022)

Bug Fixes

Chemical Structure Handling​:

  • Fixed an issue where stereochemistry inversions were occurring in the StarDrop Designer and when a structure was added to a dataset
  • Fixed an issue around rendering of hydrogens at stereocentres
  • Fixed an issue where the Show hydrogen on stereocentres preference was not being maintained
  • Fixed an issue related to incorrect behaviour when sketching hydrogen
  • Fixed an issue where stereochemistry was not being detected correctly for some structures, resulting in misassignment of Nitrogen
  • Fixed an issue where an uncharged Nitrogen could have more than four bonds without showing a valence error
  • Fixed an issue where Nova removes relative stereochemistry from result structures and parent IDs in the Chemistry Transformations workflow

Usability:

  • Fixed an issue to disambiguate duplicate data in a third-party platform integration
  • Fixed an issue where longer running models caused the models server to become unresponsive
  • Fixed an issue where creating a custom line on a scatter plot caused StarDrop to crash
  • Fixed an issue in Nova where loading some Matched Series Knowledge Bases caused StarDrop to become unresponsive

Changes

Core Application

  • EULA updated to reflect date, new products, trademarks, etc. Further, the text formatting in the StarDrop start-up was cleaned up to improve readability

SeeSAR:

  • BioSolveIT libraries were upgraded to the most recent version

Version 7.3 release notes (May 2022)

Python 2 to Python 3 upgrade

Core Application:

  • Upgraded StarDrop client to Python 3
  • Embedded Python 3 into the StarDrop dmg to ensure continued macOS support
  • Python scripts have been ported to Python 3
  • StarDrop servers (P450, Model, Auto-Modeller, Pose Generation) have been upgraded to Python 3
  • Python scripts directory has been changed to C:\\Users\\<Username>\\AppData\\Roaming\\StarDrop\\py3 on Windows and /Users/<Username>/StarDrop/py3 on macOS. This change is included to ensure that existing Python 2 scripts are not overwritten during the installation process

Cerella Integration

Core Application:

  • Suggested measurements functionality is disabled if no structure column exists in the data set
  • Issue causing unexpected white boxes on Cerella value distribution histograms has been fixed
  • An error message is now returned when incorrect credentials are entered
  • Query Interface improvements:
    • Fixed an issue where query plugin fails to retrieve some columns from PostgreSQL databases
    • Fixed an issue where the query plugin makes an unnecessary number of Cerella login requests
    • Fixed an issue where query results were not read from a NUMERIC column in PostgreSQL databases
    • Fixed an issue where data source configuration for PostgreSQL databases shows no preview columns

Interface/Usability

Core Application:

  • Long path awareness has been added to handle files with long filenames
  • Users must now specify a fragment name when sketching fragments in Nova
  • Users can now specify a StarDrop model server, but run pKa calculations on a local machine
  • Users can now open multiple model (.aim) files at the same time
  • A data set refresh button has been added to the right-hand toolbar
  • In Card View Design Preferences, users can now resize the width of the panel so that long column names are not truncated
  • The initial (default) similarity threshold has been lowered for Matched Molecular Pairs
  • Fixed a crash triggered by manipulating cards and stacks of cards in Card View
  • Fixed an issue where 3D coordinates were not saved to SD files in cases where rows contained a single conformer
  • Fixed an issue where Nova’s Matched Series Analysis misidentified a scaffold versus a substituent
  • Fixed an issue where categorical columns were not available in the Select Properties dialogue of MPO Explorer
  • Fixed an issue where a persistent “read-only” message remained in the project title bar
  • Fixed an issue where the 2D structure (molecular diagram) was not displayed in the data set for results returned from the pose generation interface
  • Fixed errors encountered when opening an SD file:
    • Files containing blank cells are now imported correctly
    • V3000 files containing SMILES property values in the data block are now imported correctly
    • Files that contain blank lines between M End and the first property are now imported correctly
  • Fixed an issue where the “remove salts” option added rather than removed a hydrogen when neutralising a charge

Version 7.2 release notes (March 2022)

New Features

Added the Inspyra module

Core Application:

  • Table View column headers now support text wrapping
  • Visualisation pop-ups can be customised and display chemical structures with multiple properties
  • Chart axes can now be logged and unlogged via a context-sensitive pop-up menu
  • Added a “6 x 4” plate option in the “assign to plate” action
  • Added an opt-in logging facility. Current log statements only cover main startup events
  • Refreshing now supports data set headers changed by the user
  • Hidden columns remain hidden when pasted into a new data set

Nova:

  • The Matched molecular pairs results table now has shown transform IDs in all relevant tables. Also additional columns in the matched pairs table now shown compound IDs.

Changes

Core Application:

  • Changed the import policy for large integers to treat them as text by default (to avoid precision errors and support compound IDs).
  • Default charts now use logged axes for properties that represent molar concentration values with unlogged units
  • Custom 2D ring templates now have priority over built in templates
  • The RingTemplates folder is now automatically generated in the user’s StarDrop folder
  • Image columns are now updated when merging or refreshing
  • The Glowing Molecule colour swatch has been removed from from designer
  • Removed case sensitivity when searching for models
  • Mol block parsing was ported from Optibrium to the OEChem implementation

Nova:

  • Changed the Nova setup wizard to no longer show results in card view by default
  • Nova was updated to use an updated Matsy knowledge base based on ChEMBL 29

Surflex eSim3D:

  • Ligand import is now restricted to a maximum of 20 compounds when importing from an SD file

SeeSAR:

  • Updated to use the latest BioSolveIT library

Derek Nexus:

  • Derek Nexus should now be installed with OpenJDK

Servers:

  • Minimum RedHat/CentOS version is now 7.4. A version check has been added to the servers installer
  • SSL protocol now set to TLS V1.2

Bug Fixes

Core Application:

  • Addressed an issue where r-group enumeration could generate molecules with values errors
  • Fixed an issue where fragments sketched in Nova do not always add successfully to the fragment library
  • Modified the charts ellipses button to pop up when there is no space to pop down
  • Modified the remove salts logic to avoid neutralising C[N+](=C)C to C[NH](=C)C
  • Modified the remove salts logic to allow neutralization of aromatic [N+]
  • Fixed an issue where an unexpected SMILES was generated when drawing deuterium
  • Fixed a scenario where deuterium would not show in Table View
  • Added the ability to create a scoring profile radar plot with axes that represent the score contribution for individual properties in the range 0 to 1
  • Fixed an issue where the first pose returned by the Pose Generation Interface server would have no score in the pose table pop-up
  • Fixed an issue when editing probabilities where ellided category names would show all ellipses and no category name
  • Fixed an issue where editing a column name after importing a CSV file leads to non-deterministic behavior
  • Fixed an occasional crash triggered when editing a data set name
  • Model search no longer ignores non-alphanumeric characters
  • Fixed a crash encountered when refreshing a data set from Python
  • Fixed a hang experienced when changing column type whilst importing a text file
  • Fixed an issue where sketched bond lengths no longer match diagram bond lengths
  • Fixed a crash encountered when right-clicking a text item in Card View
  • Fixed a crash encountered when editing a new column by adding category details
  • Improved the responsiveness of StarDrop when running models concurrently
  • Fixed a crash encountered when copying data set rows where a row contains a null data entry
  • Fixed an issue resulting in missing model results when running models concurrently

Nova:

  • Fixed ChEMBL links reported in the Nova matched series results table
  • The strictness of strict masking in R-group decomposition has been increased. Strict masking now applies a greaterThanOrEqualTo hydrogen count constraint on scaffold atoms adjacent to r-groups
  • Resolved an issue where a different number of suggestions were returned for Matched Series Analysis on macOS and Windows
  •  Fixed an issue where the chemistry transformations ‘show applicable’ option would give an incorrect transformation count
  • Fixed an issue where strict masking was not kept when a compound was pasted into the Nova wizard
  • Fixed an issue where the chemistry transformations file location would not be saved between sessions
  • Fixed a stall caused by StarDrop attempting to read a corrupt transforms.xml file
  • Fixed an issue where the Reaction-based Library Enumeration status message can get “stuck” on “<number> structures generated (100%)” progress for a significant time
  • Fixed an issue where the property used for selection in Scaffold-based Library Enumeration was not honoured
  • 2D diagram ring templates are now honoured within the Nova area and Nova setup wizards
  • Fixed an invalid SMIRKS pattern for the “Acetyl to carboxyl” transformation

BIOSTER:

  • Added the tautomer form to BIOSTER entry PYR311. There can now be multiple transformations for a single BIOSTER entry ID code
  • BIOSTER transformations are no longer read at startup to improve startup time

SeeSAR:

  • Fixed scenarios where SeeSAR flexX generates no poses

Derek Nexus:

  • Fixed a crash when running Derek models

Cerella link:

  • Fixed an issue where Cerella values were not added to cells with only measured values
  • Fixed a crash stopping a Nova run early when using Cerella models
  • Fixed a crash when running scoring using a profile that includes Cerella models
  • Cerella batch sizes can no longer be set to zero
  • Fixed an issue where Cerella access from StarDrop would expire silently after an hour of inactivity
  • Fixed the status message displayed when Cerella models fail to return results. The message no longer says ‘model calculations running’
  • Fixed a scaling issue when displaying a Cerella value distribution

Servers:

  • Fixed a typo in model_server.log
  • Fixed an issue where the servers install would not reinstate the full directory structure for custom models
  • Addressed an issue where Auto-Modeller models in the cache are lost if there isn’t enough space in the /tmp folder. If the available diskspace in /tmp is insufficient to backup the files, then the user is prompted for another location
  • Fixed an issue where StarDrop models return “No result from server” when a custom model returns “Missing dependency!”

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