Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

• Interactive 2D Overlay: Precision marquee and lasso selection on the 2D Overlay that synchronizes instantly to the Workspace, bypassing the visual clutter of the 3D binding site.
• Task Tool Smart Search: Intelligent, fuzzy search that understands user intent – instantly locating the desired panels even with typos or conceptual queries like ‘dockng’ or ‘T-cell’
• Maestro Assistant:
  • Agentic Status Indicators: Real-time status updates replace the generic loading animation, so you always know what the assistant is doing.
  • Multiple persistent chat sessions – Users can now create, rename, switch between, and delete multiple chat sessions, each maintaining its own conversation history.
  • Privacy & Transparency Controls: Users can now enable or disable the Maestro Assistant directly from Preferences, with clear in-UI communication of the current privacy mode. The updated welcome screen and persistent AI disclaimer footer reinforce that your workspace structures are never sent to the LLM.
• Surfaces: Projecting ESP and Fukui reactivity maps onto Jaguar-computed electron density isosurfaces is now a single-click action, where previously it required multiple manual steps.

Force Field

• Improvement in the accuracy of metal complexes and metal-ligand interactions of specific metal ions (Ca(II), Mg(II), Fe(II), Zn(II), Pt(II), Ir(III)) from the addition of the metals polarizable force field via OPLS5. Current application support is in relative/absolute binding FEP+ and Desmond (beta).

Target Validation & Structure Enablement

Protein Preparation

• Improved ease of use to assess clashes with crystal mates in the Diagnostics panel
• New and improved side-chain reconstruction algorithm
• Better logging of use and matching of FASTA sequences to entry
• Academic Maestro can now minimize prepared structures
• Automatically fix bonding of sulfoximines, which are often incorrectly assigned in the wwPDB/CCD 
• New option to automatically add glycosylation bonds in Maestro 
• Detect ring spears during preprocessing, displaying them in the ‘Overlapping’ Diagnostic pane

Predictive Tox Panel

• Full release of the Predictive Tox panel for screening unknown liabilities
• Open beta release of the Predictive Tox SAR panel for automated production of high accuracy atomistic models of common anti-targets using existing SAR

Binding Site & Structure Analysis

Mixed Solvent MD (MxMD)

• Save a manual step with automatic execution of SiteMap rescoring as part of MxMD simulations
• Density maps are now written in ccp4 format instead of cns

Hit Identification & Virtual Screening

Docking

• The high-accuracy MacroDock macrocycle docking workflow is now available from the command line
• Enhanced performance and efficiency in ultra-large library screening with Generative Glide (Beta): Efficiently screen ultra-large on-demand synthesizable libraries with generative AI in a fraction of the time as AL-Glide and brute force approaches

Ligand Preparation

Enumeration

• New interface to enumerate novel molecules using generative AI for molecular materials with the REINVENT method

Shape Screening

• QuickShape now stores oned_screen results as .csv

ABFEP

• Apply restraints from the interface

Lead Optimization

FEP+

• Identify the optimal simulation time to maintain accuracy with time-sliced statistics
• Share FEP+ protocols across Web Services (GraphDB), Active Learning FEP, and the FEP+ Protocol Builder for consistency with easy import and export of new FEP+ protocol configuration files
• Improved Force Field parameter merging
• Improved cycle-closure calculation performance by up to 100x by saving subcycles and graph traversal

Protein FEP

• Renamed protein “selectivity” to “affinity” to be consistent with residue scanning

FEP+ Protocol Builder

• Account for “grouped” compounds when assigning test/train splits

Macrocycles

• Macrocycle Score: New semi-automated workflow to optimize and score macrocyclic cores for a given set of conformers, with support for high-fidelity scoring with MLFFs and QM
• Macrocycle Stability: New script for using binding pose metadynamics to rank macrocyclizations for stability compared to a reference molecule
• Macrocyclize: More detailed rejection reasons are now reported for cyclization reactions
• Macrocyclize: Automated enumeration of all L- and D-amino acid attachment pairs for custom SMILES linkers in peptide mode
• Prime Macrocycle Sampling: New command-line argument, -use_random_seed, to set a random seed during sampling
• Prime Macrocycle Sampling: New command-line argument, -curvature_tol, to specify curvature restraints during sampling
• Prime Macrocycle Sampling: New command-line argument, -freeze_torsions, to specify torsions to freeze during sampling

De Novo Design

AutoDesigner – R-group Design

• Full release of R-group Design panel
• Improved AutoDesigner PDF report

AutoDesigner – Core Design

• Full release of Core Design panel
• Improved AutoDesigner PDF report

AutoDesigner – Linker Design

• Full release of Linker Design panel
• Improved AutoDesigner PDF report

Drug Formulations

• Formulation ML: Support for proteins

Crystal Structure Prediction

• Full release of Crystal Structure Prediction with support of anhydrous Z’=2 and monohydrate crystal polymorph structures: Identify stable crystal polymorphs at zero Kelvin and room temperature for a given compound through hierarchical scoring

Docs Content

• Filter tutorials based on interest
• Materials Science Panel Explorer URLs retain filter states
• New interactive GPU licensing calculator
• Collapsible sidebar menu

Education Content

• New Tutorial: Filtering and Validating Protein-Protein Docked Poses with Macromolecular Pose Filtering and MM-GBSA Residue Scanning
• New Tutorial: Introduction to Performing Metadynamics Simulations with Desmond
• New Tutorial: Screening Ultra-large Libraries with Generative Glide
• New Tutorial: Peptide Cyclization
• New Tutorial: Preparing Cyclic Peptides and Aligning them to a Reference Structure
• New Interactive Tutorials: Three interactive tutorials for AutoDesigner, a de novo design algorithm for rapidly exploring large chemical space for lead optimization
  • Set up Linker Design with AutoDesigner in Maestro 
  • Set up Core Design with AutoDesigner in Maestro
  • Set up R-Group Design with AutoDesigner in Maestro

Biologics Drug Discovery

• Non-standard amino acids script (Open Beta). A command line script to simplify and speed creation of non-standard amino acid databases for residue scanning.
• Introduced a “Fast Mode” command line option for calculating protein descriptors. The new mode speeds up computation of these descriptors by about 20% on a benchmark dataset. Especially useful for large ensembles of structures.
• Enabled light-chain template subtype selection during antibody modeling. This provides greater flexibility when selecting templates for generating antibody structural models.
• Added the lengths of antibody Complementarity-Determining Regions (CDRs) to the output of calculated protein descriptors for antibody profiling analyses.

GUI for Quantum ESPRESSO

Product: Quantum ESPRESSO (QE) Interface

• Reduced disk space usage for calculating partial charges
• Bader charge analysis (command line, requires Badar module installation)
• Parallelization over both bands and tasks (command line)
• Support for MLFF in NEB calculations

Defect Properties:

Product: MS DefectPro

• Defect Formation Energy Diagram: Analysis panel for defect energy

Microkinetics

Product: MS Microkinetics

• Improved UI for renaming reactions
• User control of displayed stage in the Final State tab

Active Learning Optoelectronics

Product: Active Learning Optoelectronics

• (+MATSCI_OPTO_AL_ML) Access to ML property prediction models
• Prediction for fluorescence

Reactivity

Product: MS Reactivity

• Reaction Network Viewer: Color scheme to identify reactants
• Nanoreactor: Setup for number of stored structures to calculate biasing potential (command line)
• Nanoreactor: Improved sampling of input conformations
• Nanoreactor: Option to use AutoTS for transition state analysis

Crystal Structure Prediction

Product: Crystal Structure Prediction

• Crystal Structure Prediction: Support for Z’=2 and monohydrates

Advanced Force Field Applications

Product: MS FF Applications

• Infrastructure: Support for metals with OPLS5 from the materials science workflows (open beta)

Transport Calculations via MD simulations

Product: MS Transport

• Diffusion Coefficient: Support for multi-component diffusion analysis
• Ionic Conductivity: Output report in the driver log for command-line access
• Thin Plane Shear: Support for viscosity prediction from velocity profile

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG

• Coarse-Grained Mapping: Standardized color scheme for Martini protein residues
• Backmapping: (+COARSE_GRAIN_BACKMAPPING) Algorithm to map coarse-grained structures to all-atom models
• Coarse-Grained FF Assignment: Automatic setup of restraints for DPD mapping
• CG FF Builder: (+CGFF_BUILDER_PARAM_NO_RESPONSE) Improvements to fitting algorithms for bond and angle terms
• CG FF Builder: Martini type guesses made visible to users
• Particle and residue names visible in MS Maestro
• Improved Martini parameters for linear polysaccharides

Complex Bilayer Builder

Product: MS Complex Bilayer Builder

• Membrane Analysis: Automated head/tail assignment independent of pdb names

Formulation ML

Product: MS Formulation ML

• Formulation ML: Support for protein
• Formulation ML: Support for aggregation functions over ingredient descriptors

Layered Device ML

Product: MS Layered Device ML

• Support for using existing device models as descriptors for new device models

Generative AI

Product: MS Generative AI

• REINVENT: Generative AI for molecular materials using the REINVENT method

MS Maestro Builders and Tools

• Disordered System: Support for barrier potential with planar interface substrates
• Interface Builder: (+INTERFACE_BUILDER) Advanced solution for building interface models
• Materials Project: API key from materialsproject.org hidden from the panel UI
• Meta Workflows: Support for order parameter analysis
• Meta Workflows: Support for bulk macromolecule relaxation protocol
• Periodic Structure Enumeration: Option to rank by electrostatic energy
• Polymer: Speed-up for building ladder polymers
• Remove Molecules from System: Speed up of up to 100X for loading CG systems
• MD Multistage: Improvements to built-in relaxation protocol ‘Semicrystalline 1’
• Solvate System: Option to prevent molecular splits across periodic boundaries
• Sugar Builder: Stand-alone model building solution for common polysaccharides

Classical Mechanics

• Droplet: Coarse-grained structures enabled
• Electrolyte Analysis: Support for 2D distribution analysis of coordinating shells
• Electrolyte Analysis: Support for cluster composition analysis
• Electrolyte Analysis: Support for residence time analysis
• Electrolyte Analysis: A tab in the viewer panel to summarize analysis results
• Electrolyte Analysis: Display of RDF and structure factor plots
• Polymer Crosslink: Support for NpγT and NpAT ensembles
• Polymer Crosslink: Support for opening multiple viewer windows
• Surface Tension: (+SURFACE_TENSION_CG) Support for coarse-grained models
• Thermophysical Properties: Option to stop after a series of failed simulations
• Thermophysical Properties: Support for varying MD timesteps by temperature
• Thermophysical Properties: Display of Calibrated Tg value from the viewer panel
• Thermophysical Properties: Support for MLFF
• Umbrella Sampling: Option to export potential of mean force to CSV output

Quantum Mechanics

• Adsorption Energy: Atomic constraints setup for molecular QM calculations
• Adsorption Energy: Improved interface for setting atomic constraints
• Optoelectronic Film Properties: Option to select the excited states of interest for ISC/RISC
• Optoelectronic Film Properties: Improved parallelization for ISC/RISC
• Optoelectronic Film Properties: Geometry optimization settings for ISC/RISC

Docs Content

• Filter tutorials based on interest
• Materials Science Panel Explorer URLs retain filter states
• New interactive GPU licensing calculator
• Collapsible sidebar menu

Education Content

• New Tutorial: Protein Characterization: Part 1
• New Tutorial: De Novo Design of Novel Compounds with REINVENT
• New Tutorial: Machine Learning for Formulation Containing Proteins
• Updated Tutorial: Droplet Contact Analysis
• Updated Tutorial: Nanoreactor
• Updated Tutorial: Liquid Electrolyte Properties: Part 2
• Updated Tutorial: Defect Formation Energy Calculation
• Updated Tutorial: Crystal Structure Prediction
• Quick Reference Sheet: Sugar Builder

Education Content

Life Science

• New Tutorial: Filtering and Validating Protein-Protein Docked Poses with Macromolecular Pose Filtering and MM-GBSA Residue Scanning
• New Tutorial: Introduction to Performing Metadynamics Simulations with Desmond
• New Tutorial: Screening Ultra-large Libraries with Generative Glide
• New Tutorial: Peptide Cyclization
• New Tutorial: Preparing Cyclic Peptides and Aligning them to a Reference Structure
• New Interactive Tutorials: Three interactive tutorials for AutoDesigner, a de novo design algorithm for rapidly exploring large chemical space for lead optimization
  • Set up Linker Design with AutoDesigner in Maestro 
  • Set up Core Design with AutoDesigner in Maestro
  • Set up R-Group Design with AutoDesigner in Maestro

Materials Science

• New Tutorial: Protein Characterization: Part 1
• New Tutorial: De Novo Design of Novel Compounds with REINVENT
• New Tutorial: Machine Learning for Formulation Containing Proteins
• Updated Tutorial: Droplet Contact Analysis
• Updated Tutorial: Nanoreactor
• Updated Tutorial: Liquid Electrolyte Properties: Part 2
• Updated Tutorial: Defect Formation Energy Calculation
• Updated Tutorial: Crystal Structure Prediction
• Quick Reference Sheet: Sugar Builder

LiveDesign

What’s New in 2026-1

• Biologics
  • Design new biologics with point mutations using natural monomers
  • Upload custom monomers via API access, and view the monomers in the sequence viewer
  • Search for a subsequence within an annotated region of a Biologics entity, by selecting the annotation and numbering scheme from pre-filled dropdowns
  • Users can now color residues by property in the sequence viewer with any model that outputs the per-residue property/properties and color scheme mapping(optional) in the specified format, or with any Freeform column that contains the output
  • The “Biologics” and “Generic Entity” options in the “Type” dropdown menu of the Advanced search panel, have been unified to “Biologics/Others”
  • View branched and cyclic peptides in the sequence viewer
• LiveDesign AI Assistant: interact with LiveDesign using an AI assistant to create Freeform and Formula columns, create and update coloring rules, perform data analyses and plot data within the Assistant, and instantly find help documentation. Note that this capability requires the LiveDesign ML plugin
• Project Dashboards
  • View a project activity stream of newly added assay data and comments using the new “Activity” section
  • Entity count statistics and recently added entities shown in the Project Dashboard will now include all entities that are searchable to the project (e.g., compounds imported to unrestricted projects), instead of entities specifically imported to the project
• Models: Column as parameter models that use a 3D column as input now have access to the favorited pose, and the pose order that is represented in the LiveReport
• UX Improvements
  • Filter out un-run, failed, and pending model cells from your LiveReport
  • Drag a compound structure from the main spreadsheet directly to the Design, Search,or Advanced search panels without opening the panel first
  • Close LiveReport tabs by clicking on them with a middle mouse button click
  • 3D Visualizer: apply Stereolabels, Element label, and Atom Number labels to the selected atoms/residues/Chains

What’s Been Fixed

• Formulas that used the Lot Registration Date column as input would fail to calculate, and cause a red error bar to appear on the LiveReport. Those formulas now calculate correctly and do not cause an error
• Icons within the main spreadsheet cells to view a pose in the 3D visualizer, or in Maestro, would disappear when the cell was resized, and now remain visible
• Adding a click-to-run model column to a matrix widget would cause the widget to crash and not show data, and now click-to-run models appear correctly in the matrix widget
• Formulas using if() statements would fail to calculate when the if() statement used experimental assay cells that contained multiple values, in which one of those values was Null. Those formulas now calculate correctly
• The “Creating New Layout” dialog did not show an option to copy an existing layout, and now correctly shows that option.
• Editing a LiveReport’s title using the “Edit LiveReport Dialog” would result in moving the LiveReport to the Project Home folder, and now editing a LiveReport with that dialog will not move the LiveReport to a different folder
• Formatting option buttons on the Configure Matrix Widget dialog overlapped, which prevented accessing some formatting options, and now the buttons do not overlap
• Experimental assay data would show dashed lines underneath experimental values within the spreadsheet cells, and now do not show dashed lines
• The aggregateMax() and aggregateMin() formula functions now work for date columns
• Multi-chain or branched peptides are now accurately identified with incremental peptide numbers in their identifiers in sequence viewer.
• The sequence viewer now shows a message when TCRs with unsupported numbering schemes are used, and suggests to move to a supported numbering scheme for TCRs in the sequence viewer.
• When 3D visualizer is drilling down from the sequence viewer, selecting another entity in the sequence viewer does not reset the existing residue selection in the sequence viewer and 3D visualizer
• Parameterized models that used another model’s image columns as input would not calculate results, and now correctly calculate
• Recalculating a deleted model return would result in a permanently flashing cell, and now the cell will correctly show a Failed message
• When models returned a 3D output of type “other”, that 3D output was not accessible to other parameterized models, and now is accessible
• LDClient: the method get_models_by_name now includes an option to ignore archived models