Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

• Added nonstandard nucleotide support: Right-click any DNA or RNA residue to mutate it to a nonstandard nucleotide via a searchable panel with 2D structure preview
• New GPCR Workspace Preset for annotated G protein-coupled receptor visualization
• Revamped surface management including comparison of multiple surfaces in the surface toggle: Select multiple surfaces to see a sortable, side-by-side comparison of Area, Isovalue, Sigma, and more in the Info tab. The panel can now be undocked and floated freely
• Simplified Maestro to LiveDesign export for Biologics: Redesigned the Generic Entity export panel (“Biologics/Others”) with two clear workflows, Register New Entities (with HELM-based deduplication) or Append 3D Data to Existing Entities
• Streamlined ability to “Load Selection” for Workspace Interactions: Select atoms in the Workspace, click “Load Selection” in the Interactions dropdown to instantly display their interactions without manually configuring “Other” definitions
• Standalone Map Import in Get PDB: Diffraction data and EM maps are now imported as standalone entries grouped alongside their structures in the Project Table
• New “Other Modalities” Task Tool category with “Degraders” and “Macrocycles” subcategories, grouping specialized panels for easier discoverability
• More intuitive clipping plane zoom controls: The clipping plane view now zooms with the Workspace by default, and new right-click menu options let you toggle clipping plane behavior without navigating to Preferences
• Redesigned Preferences Directories page: Cleaner layout with Browse buttons, clearer terminology, automatic detection of SCHRODINGER_TEMP_PROJECT overrides, and Windows-only sections hidden on Mac/Linux
• “Check for update” option added to the Help menu
• Dramatic improvements in the MSV pairwise sequence alignment

Target Validation & Structure Enablement

Protein Preparation

• Annotate GPCRs automatically during structure preparation
• Selenomethionines are now converted to methionines by default during preparation
• Command-line options overhauled for greater simplicity and to match the Maestro interface’s defaults
• Disable/Hide unusable options in Academic Maestro
• Removed the -noimpref flag from CLI consistent with deprecation of the impref minimization scheme
• Warn users if sidechain atoms could not be rebuilt with the new sidechain rebuilding method

Cofolding

• Maestro panel automatically evaluates and corrects ligand bond orders in prepared models
• Removed confidence based trimming of residues in post-processing
• Full multiple sequence alignment used to construct homology models viewable in the MSV

Predictive Tox Panel

• Added thirteen new GPCR targets to panel, 5HT1B, 5HT2B, 5HT2C, ACM4, ADA2A, ADRB1, ADRB2, APJ, DRD3, OX2R, DRD2, ADORA1 and CNR2
• Added five new bromodomain targets to panel, BRD2 BD1, BRD2 BD2, BRD4, BD1, BRD4 BD2, and CBP
• Added three new nuclear receptor targets to panel, RXRa, AR, ER Beta
• All panel targets supported in both Predictive Tox and Predictive Tox SAR Panels

Binding Site & Structure Analysis

Binding Site Characterization

• First release of Rapid Binding Site Similarity (RBSS)
  • Compute binding site similarities for a protein against all binding sites in the PDB in seconds
  • Compute binding site similarities for a protein against user-provided libraries of binding sites
  • Uses coarsened molecular interaction fields (MIFs) computed on a grid to represent the preference for different functional groups to occupy locations on a grid including, aromatic, hydrophobic, h-bond acceptor, h-bond donor, and positive and negative charges

Desmond Molecular Dynamics

• Speed simulations up to ~66% with support to adjust Hydrogen Mass Repartitioning (HMR)
• Seven new mixed lipid bilayers are now supported by the System Builder

Mixed Solvent MD (MxMD)

• Specify probe target concentration in the input to simulations (command line only)

Hit Identification & Virtual Screening

Active Learning Applications

• Automatically generate the group dG prediction for multi-state protomer groups after including all protonation states of the selected ligands
• Specify the number of lambda windows separately for charged and uncharged ligands for ABFEP and final rescore ABFEP steps
• Apply positional restraints in AL-ABFEP simulations
• AL-FEP+ enriched substructures in the report file now exclude the common core
• AL-ABFEP extends the final rescore ligands instead of running them from scratch to save computation time when ABFEP is run on GraphDB

Docking

• Glide uses ZMQ job distribution (-mq option) by default for faster wall clock turnaround of docking jobs with multiple subjobs through better subjob scheduling

Lead Optimization

RetroSynth

• New combined Maestro RetroSynth setup and analysis panel: Perform and analyze retrosynthesis routes generated by RetroSynth in Maestro or LiveDesign

FEP+

• New ABFEP scanning mode: Perform calculations up to 5x faster with slight loss of accuracy using half lambda windows, 2 ns simulation times, and a truncated receptor
• New Interaction Energy plot fragment decomposition feature: Get a richer understanding of how specific compound fragments interact with the receptor
• Support added for seven new mixed lipid bilayers
• Create “write” submission commands from Maestro interface to Web Services
• PoseBuilder can now generate covalent protein-ligand complex poses ready for covalent FEP+ from command line or in LiveDesign

Protein FEP

• Compute pH-dependent affinities directly from the Maestro interface
• Perform FEP Residue Scanning (FRS) at large scale : New workflow that splits mutations into multiple batches and automatically runs them in parallel before merging results into a single out.fmp file

E-sol

• New panel to setup, execute, and analyze predictions if experimental Efflux ratio data is available

FEP+ Protocol Builder

• Unified Panels that can set up and analyze FEP+ Protocol Builder jobs
• Explore different membrane types as a new parameter
• Command line ‘-prepare’ mode that generates protocols without submitting them

Quantum Mechanics

• Predict compound atropisomerism and analyze key rotational barriers with a new Maestro panel
• Provide an at-a-glance view into the simulation settings and results of an AutoTS calculation in an automatically generated html report

Spectroscopy

• 13C NMR heavy-atom corrections for C-F are now supported

Semi-Empirical Quantum Mechanics

• g-xTB can be invoked from Jaguar after installation by the user (must activate the XTB_GXTB feature flag)

Macrocycles

• New macrocycle docking panel for launching MacroDock jobs
• New sampling options in the Prime macrocycle sampling panel
• Improved macrocycle conformer generation for Glide and IFD-MD docking for ring systems that contain certain nitrogen chemistries
• More thorough sampling of complex multicycles such as vancomycin in Prime macrocycle sampling (Prime-MCS)
• Prime macrocycle sampling (Prime-MCS) conformers are now all automatically aligned to a single reference frame
• Macrocycle docking workflow (MacroDock) is ~2.5x faster than reported in the original publication, reducing the median CPU runtime to under 1 hour per compound while maintaining a success rate of ~80%
• Macrocycle docking workflow (MacroDock) now supports docking with experimental density maps
• New script for batch docking into the same ligand site (macrocycle_batch_docking.py)

Drug Formulations

Crystal Structure Prediction

• Full release of Crystal Structure Prediction supporting salts, solvates, and co-crystals for confident form selection in solid-state development: Computationally screen at scale to identify the most stable, manufacturable crystal form before committing to experiments and secure your formulation strategy

Docs Content

• Learning Paths have been completely redesigned for improved usability

Education Content

• New Learning Path: Cyclic Peptide Modeling
• New Tutorial: Handling Non-standard Amino Acids
• New Tutorial: Modeling Blood-Brain Barrier Penetration Using E-sol
• Redesigned Tutorial: A Chemist’s Guide to Maestro
• Updated Tutorial: Evaluating Large Ligand Libraries with Active Learning Glide
• Updated Tutorial: Introduction to Performing Metadynamics Simulations with Desmond
• New Interactive Mini-tutorial: Rapid Binding Site Similarity Search (embedded in the Panel Help)

Biologics Drug Discovery

• Simple, high-throughput creation of a nonstandard nucleotide library for use in Maestro for DNA/RNA/oliogo design
• New output files from PIPER enables streamlined analysis of docked poses reducing post-processing effort

GUI for Quantum ESPRESSO

Product: Quantum ESPRESSO (QE) Interface

• Support for dipole correction setup from the input *.cfg file (command line)
• Option to visualize reaction profile as a function of NEB inter-image distance
• Multi-threaded MLFF calculations for NEB calculations (command line)
• GPU support for NEB calculations with MLFF (command line)

Microkinetics

Product: MS Microkinetics

• (+MKM_ELECTROCATALYSIS) Support for multistage workflow for electrocatalysis

Active Learning Optoelectronics

Product: Active Learning Optoelectronics

• Active Learning Optoelectronics: Access to ML property prediction models
• Active Learning Optoelectronics: Access to AutoQSAR/DeepAutoQSAR models

Reactivity

Product: MS Reactivity

• Nanoreactor: Option to adjust biasing potential
• Nanoreactor: Simplified UI for improved user experience
• Nanoreactor: Improved settings for enhanced reaction discovery
• Nanoreactor: AutoTS transition state frequencies reported in the output
• Reaction Network Profiler: Prevention of atom clashes during input preparation

Reactive Interface Simulator

Product: MS RIS

• Solid Electrolyte Interphase: Improved support for ions with zeroth order bonds

Advanced Force Field Applications

Product: MS FF Applications

• MLFF Fine-tuning: Solution to fine-tune MPNICE MLFF models and use them through in Schrödinger Suite
• MLFF Calculations: Support for vibrations and phonon calculations

Transport Calculations via MD simulations

Product: MS Transport

• Ionic Conductivity: Option to apply linear response theory for predictions
• Thin Plane Shear: Improved definition of plane for shear

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG

• Backmapping: Tool to map coarse-grained systems to atomic representations
• CG FF Assignment: Support for encrypted force field files
• CG FF Builder: Improved selection of data for plotting in viewer
• CG FF Builder: Improved fitting of valence terms
• Coarse-Grained Mapping: Generation of Martini FF file for selected structures
• Visualization of CG protein backbone as tube in the workspace

Materials Informatics

Product: MS Informatics

• MPNICE Embeddings: Machine learning with MPNICE embeddings as descriptor

Layered Device ML

Product: MS Layered Device ML

• OLED Device ML: Option to use pre-trained ML model output as descriptors for new models
• OLED Device ML: Support for tandem OLED devices
• OLED Device ML: Visualization of feature importance from the viewer panel

Denovo ML

Product: MS Denovo ML

• REINVENT: Updated job submission protocol for improved speed

MS Maestro Builders and Tools

• Agentic Workflow: (+MATSCI_AGENTIC_WF) Language-model-based solution to create custom Meta Workflows
• Crystal Structure Prediction: Support for salts and solvents
• Free Volume Analysis: Reduced memory use for the analysis
• Import Slabs: Addition of 25 pre-built slab models
• Interface Builder: Model builder for bulk interfaces and grain boundaries
• Structured Liquid: Redesigned UI for improved user experience
• Sugar Builder: (+NEW_SUGAR_BUILDER_PANEL) Option to build with glycosylation patterns

Classical Mechanics

• Droplet Contact Angle: Support for MLFF
• Electrolyte Analysis: Option to merge neighboring ion clusters for analysis
• Evaporation: Speedup of up to an order of magnitude for coarse-grained systems
• Support for TIP4P water model with OPLS_2005
• MD Multistage: (+MULTISTAGE_MD_CONCATENATE) Option to concatenate Brownie stage with other stages
• Polymer Crosslink: Reduced memory use of free volume analysis
• Thermophysical Properties: Reduced use of disk space

Quantum Mechanics

• Optoelectronic Film Properties: Option to set T1 geometry from DFT or TDDFT
• Optoelectronic Film Properties: Speed up for ISC/RISC reorg energy calculation
• Reaction Network Viewer: Single output for multiple rxn networks (command line)
• Reaction Network Viewer: Option to view structures in the workspace
• Reaction Network Viewer: Option to save reaction network images

Education Content

• New Tutorial: MLFF Fine-Tuning
• New Tutorial: Building Epitaxial Interfaces
• New Tutorial: Protein Characterization: Part 2
• New Tutorial: Machine Learning with MPNICE Embedding
• New Tutorial: Crystal Structure Prediction: Part 2
• Updated Tutorial: Optoelectronics Active Learning
• Updated Tutorial: Ionic Conductivity
• Updated Tutorial: Liquid Electrolyte Properties: Part 2
• Updated Tutorial: Automated Dissipative Particle Dynamics (DPD) Parameterization
• Updated Tutorial: Nanoemulsions with Automated DPD Parameterization
• New Quick Reference Sheet: Coarse-Grained Backmapping

Education Content

Life Science

• New Learning Path: Cyclic Peptide Modeling
• New Tutorial: Handling Non-standard Amino Acids
• New Tutorial: Modeling Blood-Brain Barrier Penetration Using E-sol
• Redesigned Tutorial: A Chemist’s Guide to Maestro
• Updated Tutorial: Evaluating Large Ligand Libraries with Active Learning Glide
• Updated Tutorial: Introduction to Performing Metadynamics Simulations with Desmond
• New Interactive Mini-tutorial: Rapid Binding Site Similarity Search (embedded in the Panel Help)

Materials Science

• New Tutorial: MLFF Fine-Tuning
• New Tutorial: Building Epitaxial Interfaces
• New Tutorial: Protein Characterization: Part 2
• New Tutorial: Machine Learning with MPNICE Embedding
• New Tutorial: Crystal Structure Prediction: Part 2
• Updated Tutorial: Optoelectronics Active Learning
• Updated Tutorial: Ionic Conductivity
• Updated Tutorial: Liquid Electrolyte Properties: Part 2
• Updated Tutorial: Automated Dissipative Particle Dynamics (DPD) Parameterization
• Updated Tutorial: Nanoemulsions with Automated DPD Parameterization
• New Quick Reference Sheet: Coarse-Grained Backmapping

LiveDesign

What’s New in 2026-3

• Biologics

  • Design new Antibody-Drug Conjugates: create ADC entities in the Entity Builder using four new templates supporting monospecific and bispecific antibodies, with separate or combined linker and payload components.

  • Multi-point and combinatorial residue substitution: choose Single Point, Multi-point, or Combinatorial mutation type to enumerate all combinations across multiple positions in a single run, with up to 10,000 unique combinations per request; progress notifications link directly to newly inserted rows.

  • Monomer Database Viewer: browse, search across name, symbol, and other fields, sort, filter, and manage monomers in a dedicated viewer supporting libraries of 30,000 or more monomers, with alias support for HELM strings and validation on batch upload

  • Subsequence search across adjoining annotated regions: search for sequences spanning region boundaries — such as a CDR3 and FR4 junction — by selecting multiple structural annotations in Advanced Search and enabling “Search across boundaries.”

  • Import 3D structure data from Maestro: export 3D data from Maestro directly to generic entities and biologics, with options to create a new 3D column, append to an existing column, or overwrite existing data.

  • Sequence Viewer: filter to constant domains and hinge regions: show only CH1, CH2, CH3, CL, or hinge region residues for faster antibody developability and manufacturability checks; CDR regions are now shown by default for antibody entities.

  • Sequence Viewer: alignment with standard and custom substitution matrices: choose from BLOSUM62, PAM250, BLOSUM45, BLOSUM80, or GONNET, upload a custom CSV matrix, or align by residue number using Kabat or other antibody numbering schemes.

• Project Scaffolds

  • Apply project-level scaffolds in the R-group decomposition panel alongside LiveReport-specific scaffolds, with project scaffolds given preferential compound matching; publishing an updated scaffold list automatically syncs changes and recalculates R-group decomposition across all open LiveReports.

  • Manage project scaffolds from a new Project Administration tab in the Project Dashboard; renaming a scaffold is immediately reflected in R-group decomposition results across all open LiveReports.

• Forms: Multi-Entity Matrix Widget: view compound structures and data side-by-side in a transposed table format, with structures as columns and properties as rows, and add custom labels for each row.

• Project Dashboard: filter the Activity stream by specific published comment columns or by users in the project; access the Dashboard directly from the LiveDesign header by clicking the LiveDesign logo.

• Plots

  • 2D Heatmap (Beta): visualize data across two categorical dimensions with aggregation modes (Mean, Median, Min, Max, or Count) and support for MPO and other advanced coloring rules.

  • Date-based grouping in Box Plots, Scatter, and Line charts: group date-type X-axes by Day, Week, Month, Quarter, or Year to view trends over time, with an option to display data aggregated or unaggregated per time bin.

• SAR Analysis: option to remove entity structure coloring: toggle “Show Structure Coloring” off in the compound column menu to remove R-group decomposition color overlays while preserving scaffold alignment; the toggle is per-LiveReport and session-only, and a server property controls the default state for all users.

• System Health Tool (Beta): monitor LiveDesign system health from a centralized dashboard showing model task queue depth, LiveReport execution queue metrics, task engine status by queue type (Sync, Async, Fast, and Realtime), and JVM heap usage, with icons and tooltips on each metric tile.

• UX Improvements

  • Recalculate Failed Only: the model column menu now includes a “Recalculate Failed Only” option to rerun only cells with failed results, without filtering the LiveReport first.

  • Adding a compound via the design sketcher now selects the newly added row, consistent with search-by-ID and advanced search.

  • Admin users can configure a server property to allow regular users to apply templates to LiveReports they do not own or that already contain data.

  • The Visualize panel tab now includes a Close All option for open plots and tools; right-clicking a plot tab shows context menu options to open, pop out, or close it without switching to the tab first.

  • Renaming a plot now opens an in-app dialog instead of a browser popup, and hovering over a plot tab shows the full plot name in a tooltip.

  • Plot legends repositioned from their default location now appear correctly in exported PNG and SVG files.

  • Residue-level sync selection between the Sequence Viewer and 3D Visualizer is now enabled by default.

  • The property column dropdown in the Generic Entity import dialog now includes a search field to quickly locate columns by name.

What’s Been Fixed

Advanced Search

• Advanced Search: changing AND/OR logic operators in the complex view would be ignored during the subsequent search, and now correctly reflects the updated logic.

• Advanced Search: entering an invalid sequence in a subsequence query would silently search using the previously entered valid sequence, and now correctly disables the search button when the sequence format is invalid.

• Advanced Search with child entity queries would return parent entities whose only matching child was archived, and now correctly excludes archived child entities from search matching.

• Dragging and dropping a structure into the filter panel would load the structure in the sketcher but leave the ‘Add’ button disabled, requiring a manual edit before the filter could be applied; the ‘Add’ button is now enabled as soon as a structure is loaded.

• Substructure searches in Advanced Search would return the same entities regardless of which dataset was selected, and now correctly filter results to the chosen dataset.

• The Structural Annotation and Numbering Scheme dropdowns in Advanced Search would appear misaligned and incorrectly sized in complex view, and now display with consistent alignment in both simple and complex view.

• Deleting a query group that contained sub-queries in Advanced Search would throw an error and cause subsequent queries to fail; query groups with sub-queries can now be deleted without errors.

• Advanced search by ID would return entities that matched the All IDs column, and now correctly returns only entities where the ID matches the ID column.

• Advanced search queries would get stuck in a permanent error state when changes were made concurrently, forcing users to start over in a new LiveReport, and now handle concurrent updates without getting stuck.

• The ‘Presence in LiveReport’ advanced search condition would expose Global Project LiveReports to users in Hyper Restricted Projects via the ‘Shared with Me’ option, and now only shows LiveReports within the restricted project.

Filters

• A deleted condition in the complex filter panel would reappear after a browser refresh when the filter expression contained a validation error, and now deleted conditions are correctly persisted. Invalid filter expressions also now show a friendly error message instead of repeatedly showing a loading state.

Authentication

• During SSO login, users would be redirected back to the login page and need to click the ‘Login with SSO‘ button a second time to successfully sign in, and now log in on the first attempt.

• Users on servers with the refresh token filter enabled would receive 401 errors on login or be frequently logged out, and can now log in and maintain sessions reliably.

• Multiple users starting sessions concurrently would receive 502 errors, and now start sessions reliably even under high concurrent load.

• When LiveDesign attempted to refresh a user access token and the authentication service was temporarily unreachable, the timeout was treated as an authentication failure and the user was logged out; LiveDesign now retries the token refresh request over a short window before treating the disruption as a failure, so brief authentication service unavailability no longer causes unexpected session termination.

Biologics

• In Entity Builder, using ‘Get from Selection’ on a Monospecific Antibody in a LiveReport would show an entity type mismatch error, and now correctly populates the selection.

• In the Monomer Database viewer, clicking a monomer row after applying a filter would display the details of a different monomer; the correct monomer details are now shown when clicking a filtered row.

• Copying a monomer SMILES from the Monomer Database tooltip would include extra whitespace that caused SMILES filter searches to return no results; copying SMILES from the tooltip now correctly returns matching monomers when used as a filter.

• Editing a reactant in the Reaction Enumeration sketcher would change Enhanced Stereo labels to Absolute (R or S) labels; Enhanced Stereo labels are now preserved when structures are edited and re-opened in the sketcher.

• The monomer storage tool is now consistently named Monomer Database throughout the interface.

Freeform Columns

• Bulk copying values into a Freeform column would cause the LiveReport to show a white screen until the browser was refreshed, and now applies the copied values correctly without a page reload.

• The Freeform column audit trail tooltip would display values from a previously hovered cell when a network error occurred; the audit trail now always shows the correct content for the currently hovered cell.

• Double-clicking OK when saving a comment in a Freeform Comment column would create two duplicate comment entries, and now correctly creates only one.

• Deleted Freeform Comment columns would still show an Edit Column option in the column menu and allow editing column details, and now deleted columns are correctly view-only.

• The Comments Panel would show ‘No entities selected’ when entities were selected but the LiveReport had no Freeform Comment columns, and now correctly indicates that no comment cells are selected.

Forms View

• In Forms View, clicking an entity in the parent widget would require a second click before the child widget updated with the drilled-down entity; the child widget now updates on the first click.

• Forms matrix widget labels now correctly save all rich text formatting including font size, font color, italic, underline, strikethrough, and horizontal alignment.

• Switching between spreadsheet and Forms view in large LiveReports is now faster.

• Kanban tiles would not have a drop zone for dragging to a new vertical or swimlane when the vertical column was not displayed on the tile; drag and drop now works regardless of which columns are shown on the tile.

• Kanban tiles in Forms View now correctly display biologic entity images instead of showing a blank cell.

• Global form layout templates could be overwritten, renamed, or deleted from non-Global projects, and now global templates are protected from modification outside the Global project.

LiveReport

• LiveReports containing date columns with many empty cells would take an unusually long time to load due to slow date parsing; loading performance for these LiveReports is now significantly faster.

• LiveReports containing multiple real generic entities that share a virtual entity would fail to load, and now calculate correctly.

• Duplicating a LiveReport with hundreds of columns and unpublished Freeform columns would take over a minute, and now completes in seconds.

• Limited assay columns would lose their reference to the parent assay column and become impossible to publish, and now correctly retain that reference.

• Limited assay columns in a batch group would fail to ungroup via the Column Ungroup option or the Data & Columns tree Ungroup option, and now ungroup correctly through both methods.

• Running a model on parent entities that have child entities would cause the child entities to appear as separate rows in the LiveReport, and now only the parent entities are affected.

• Copying cell values from a LiveReport with frozen rows would add extra blank lines to the clipboard equal to the number of frozen rows; cell values now copy without extra blank lines.

• The vertical scrollbar handle in the LiveReport spreadsheet would lag behind the cursor when dragging quickly, preventing users from reaching the bottom of large LiveReports, and now scrolls smoothly and responsively.

• The Show Hidden Rows dialog would display an incorrect entity alias when multiple ID column aliases existed, and now shows the correct ID column alias.

• Clicking OK in the project picker after searching for a project by name would fail to switch to that project, and now correctly navigates to the selected project.

• Clicking the Assay Viewer link in an assay data tooltip would fail to open the tool and could leave it inaccessible until the page was refreshed, and now the Assay Viewer opens correctly from the tooltip.

• Files with underscores in their names were not searchable in the Manage Files dialog, and now appear correctly in search results.

• Adding a design from the sketcher to a LiveReport could take more than 20 seconds and sometimes fail entirely, and now is added immediately.

Models

• Models using the {ORIG-SDF-FILE} macro in their protocol commands would fail to generate the required input file when run against Generic Entity rows, and now correctly produce the input file for all entity types.

• Model result cells would sporadically show as failed even when the model had completed with data, requiring a manual model rerun to display the results; cells now correctly show model results without needing a rerun.

• Click-to-run models would fail to submit when a dependent model was triggered simultaneously, and now correctly submit their tasks.

• Empty input cells passed to parameterized models would inconsistently appear as ‘[]’ instead of an empty string in the model’s CSV input, and now consistently use an empty string.

Admin Panel

• On Admin Panel deployments with a large number of parameterized models, the model list page would stretch horizontally to render all pagination page numbers in a single row, making the layout difficult to use; the pagination control now displays a condensed set of links, keeping the table compact regardless of model count.

• Users with the LiveDesign User role were unable to open the Tasks dialog on deployments with a large number of unrestricted projects (~250 or more); the request line size limit has been increased to allow the task page to load on deployments with 400+ unrestricted projects.

• Users with the UserAdmin role would fail to save edits to project properties, including project description, Therapeutic Area, and Group permissions; UserAdmin users can now edit and save project settings as expected.

• Admin Panel actions on the Projects and Groups pages would return 403 CSRF token errors when the same user performed edits simultaneously from multiple browsers or tabs; this issue has been resolved.

• The LiveDesign logo in the Admin Panel header would become distorted when the browser window was resized to a smaller width; the logo now displays correctly at all viewport sizes.

Project Dashboard

• Entity and R-group structure images on plot axes were not visible when plots were added to the Project Dashboard; plots on the Project Dashboard now correctly display structure images on their axes.

• Plots with entity or R-group images on the axes would display all compound images grouped into one when added to the Project Dashboard; compound images on dashboard plot axes are now grouped and displayed individually.

• Pinned tooltips on Project Dashboard plot widgets would disappear when clicking a different data point, and now remain visible.

• Radar plots are now excluded from the Project Dashboard, where they could not display data because they depend on user selection; a message indicates that radar plots are not supported on the Dashboard.

Plots

• 3D scatter plots would fail to render after a library upgrade; 3D scatter plots now display correctly across all column types, aggregation modes, and views.

• Hovering over data points on scatter or line plots with aggregation mode applied would not show a tooltip, and now correctly displays aggregated value information on hover.

• Exporting plots containing entity or R-group column axes to SVG or PNG would produce files without the structure images; exported plot files now correctly display entity and R-group images.

• Chart legends would be cut off when exporting plots as SVG or PNG, and now appear fully visible in the exported file.

• Holding and dragging the mouse to select compounds in a 1D heatmap would not select entities within the drag area, and now correctly selects all entities in the selection region.

• Compound images shown along a plot axis would expand downward and get cut off by the docked tooltip, and now display correctly above the tooltip.

• The plot options ‘more’ button would get cut off with certain browser or OS scaling settings or when long column names were selected, and now remains fully visible in all configurations.

• The Rename dialog for plots now displays the current plot name alongside a field for the new name, with the dialog title updated to use standard capitalization.

• The 1D heatmap would inconsistently display entity identifiers instead of the configured corporate ID, and now consistently shows the correct ID column identifier.

• The visualization panel would go blank and become unresponsive for viewer-access users when clicking a dropdown on any plot or the 3D Visualizer, and now correctly displays the dropdown options.

• The Plot Options modal could be dragged so far up the screen that its title bar and close button were hidden behind the browser’s address bar; the modal now stays within the visible viewport.

Sequence Viewer

• Selecting an entity from the LiveReport grid would not load it into the Sequence Viewer when in Forms View, and now correctly loads the selected entity.

• In the Sequence Viewer, residue conservation values shown in tooltips would change when switching the residue display format between FASTA and Monomer-DB, and now conservation values remain consistent regardless of the display format selected.

• The Sequence Viewer alignment dropdown option was incorrectly labeled ‘By Numbering Residue’ and has been corrected to ‘By Residue Number.’

• Sequence Viewer data column values would become hidden when scrolling horizontally past the sequence canvas, and now remain visible throughout horizontal scrolling.

• Sequence Viewer: non-natural monomers (X) in the Logo plot would be colored using the active color scheme, and now correctly use their assigned natural analog color or a neutral gray.

• Sequence monomer fonts in the Sequence Viewer would change when applying ‘Differing Residues’ coloring in Firefox, and now remain consistent regardless of coloring mode or selection state.

• The ‘Processing X Sequences’ notification in the Sequence Viewer would count all loaded sequences rather than only the visible ones, and now correctly reflects only the visible sequence count.

• Clicking on annotation dropdown labels such as CDR1, CDR2, and CDR3 in the Sequence Viewer would not open the dropdown, and now correctly opens it.

• CDR filtering in the Sequence Viewer would only work for the first two chains of a multi-chain antibody, and now works correctly for antibodies with any number of heavy and light chains.

• Residues matching the reference sequence would stop displaying as dots when CDR filtering was applied, and now display consistently as dots regardless of filtering.

3D Visualizer

• In the 3D Visualizer, loading a saved scene would not re-orient the structure to the captured view, and saving subsequent new scenes would also fail; saved scenes now correctly restore the saved orientation.

• The Residue Type color scheme in the 3D Visualizer now correctly colors unknown and non-natural amino acid residues with a distinct default color.

• 3D Visualizer: selecting multiple residues one by one on the canvas would only reflect the first selection in the Hierarchy panel, and now all selected residues are highlighted correctly.

• 3D Visualizer: entity checkboxes in the Content panel now work independently when the same attachment is loaded in multiple cells.

• 3D Visualizer: adding non-polar hydrogens to a ligand would cause atom labels to change color, and now labels retain their correct color.

• In the 3D Visualizer, entering measurement mode while structure alignment was active would disable all selection types; the measurement tool is now automatically disabled when structure alignment is in progress.

• Residue labels in the 3D Visualizer would disappear when switching background colors, and now remain visible after background color changes.

• 3D Visualizer: exporting a structure to .mae or .maegz would include previously removed atom labels, and now only the currently visible labels appear in the exported file.

• The Numbering Scheme dropdown in the 3D Visualizer’s Hierarchy tab would truncate ‘Enhanced Chothia’ and not show the full name, and now correctly displays all numbering scheme names in full.

• In the 3D Visualizer, labels applied to binding site residues would be removed when a ligand was toggled off and back on, and now labels are correctly restored on all residues after toggling.

• Residue labels in the 3D Visualizer would turn white when changing style presets on a black background, and now retain their correct color.

• 3D Visualizer now loads structures faster by requesting compressed attachment data from the server and caching structures across the browser session.

• In the 3D Visualizer structure alignment panel, pressing the Back button in custom atom selection mode would clear the reference selection on the canvas, and now correctly restores the previous selection.

• The ‘Carbons Only’ checkbox in the 3D Visualizer’s canvas override color panel would appear enlarged with missing padding, and now displays at the correct size.

Ligand Designer

• Ligand Designer: overlay structures were editable and allowed atoms to be selected and modified, and now remain non-editable as intended.

• Ligand minimization would silently succeed for structures with invalid bond orders, and now correctly reports a failure for structures that cannot be processed.

MMP

• The View button for a proposed compound in the MMP analysis panel would not scroll to and highlight that compound in the LiveReport; the button now correctly brings the compound into focus.

• The MMP delta plot X-axis would start at zero instead of the first transformation ID, and now correctly starts at 1.

SAR Analysis

• Saving R-groups to a new LiveReport after R-group decomposition would produce an empty LiveReport when aromatized structures were generated, and now correctly saves all R-groups.

Enumeration

• Reaction enumeration would occasionally fail with no products appearing in the target LiveReport and no indication of what went wrong; the failure now surfaces a descriptive error message.

Export

• Exporting a LiveReport containing limited assay columns would omit the ‘(Limited)’ suffix from column names in SDF, PPTX, and XLS exports, and now correctly includes the suffix to match the display in the LiveReport grid.

• Exporting a LiveReport containing generic entities to XLS or XLS Aligned format in row-per-pose mode would fail with an error, and now exports successfully.