Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

• Redesigned Surface Manager – Control complex visualizations effortlessly with a modern, persistent interface that allows for real-time, non-modal editing of surface styles, colors, and transparency
• Persistent measurements – Geometric measurements now persist with the entries, allowing for uninterrupted structural comparison across multiple conformers and states
• Standalone density map import – Accelerate Cryo-EM and crystallography workflows with direct, standalone density map import
• Maestro Assistant modes (open beta) – A context-aware AI partner that intelligently toggles between ‘Ask’, ‘Execute’, and ‘Auto’ modes to seamlessly bridge documentation and direct action

Binding Site & Structure Analysis

Mixed Solvent MD (MxMD)

• Added support to command line MxMD driver to seamlessly execute all simulations and compile results from combined MxMD/SiteMap cryptic pocket identification workflow

WaterMap

• WaterMap now supports use of the OPLS_2005 forcefield and TIP4P water model

Hit Identification & Virtual Screening

Docking

• Understand, optimize, and troubleshoot native redocking experiments with new Docking Report to maximize docking performance

Lead Optimization

FEP+

• GraphDB/Web services can optionally download only the primary FMP file and not the FMPdb reducing time to analyzing results
• FEP+ workflows now support execution on cost-effective preemptible nodes
• Use 2D Sketcher to define Core SMARTS for FEP+
• Improved handling of categorical assay data in FEP+ statistical analysis

FEP+ Protocol Builder

• Sample three levels of salt concentrations in protocol optimization
• Sample automatic membrane placement in protocol optimization

FEP+ Pose Builder

• Automatically create accurate and clash-aware FEP-ready poses with FEP+ Pose Builder: Generate high-quality ligand alignments faster to run FEP+ at scale with an automated workflow designed for unbiased selection and robust atom-mapping
• LiveDesign FEP+ Pose Builder protocol now supports generating FMP files for cycle-closure FEP calculations

Quantum Mechanics

• Employ xTB and MLFFs including QRNN, MPNICE, and UMA in AutoTS from command line for shorter calculation times
• Faster batch calculations by optimized CPU core assignments for all multithreaded Jaguar batch calculations

Spectroscopy

• New corrections for C-Br and C-I bonds in 13C NMR spectra

De Novo Design

AutoDesigner – R-group Design

• Explore large chemical spaces to identify optimal R-groups with new AutoDesigner R-group Design Panel now accessible by setting a feature flag
• Added optional QED score (Quantitative Estimate of Drug-Likeness) for AutoDesigner R-group Design ideas

AutoDesigner – Core Design

• Explore large chemical spaces to identify optimal core replacements with new AutoDesigner Core Design Panel now accessible by setting a feature flag
• Added optional QED score (Quantitative Estimate of Drug-Likeness) for AutoDesigner Core Design ideas

Education Content

• Introducing a new, more interactive tutorial experience, letting users intuitively click through the steps of a workflow right in the tutorial. This approach is being piloted in two tutorials.
  • Updated Tutorial: Structure-Based Virtual Screening Using Glide
  • Updated Tutorial: Introduction to Structure Preparation and Visualization
• Fully re-worked learning content on Antibody Modeling:
  The “Antibody Visualization and Modeling in BioLuminate” tutorial has been replaced by a new suite of tutorials organized in a learning path together with other helpful resources.
  • New Learning Path: Antibody Modeling
  • New Tutorial: Antibody Structure Prediction and Visualization with BioLuminate
  • New Tutorial: Humanizing Antibody Structures with BioLuminate
  • New Tutorial: Antibody – Antigen Docking with PIPER
  • New Tutorial: Improving Antibody Stability/Affinity Using MM-GBSA Residue Scanning
• New Tutorial: Generating ternary complex structures to enable rational design of targeted protein degraders
• Updated Tutorial: BACE1 Inhibitor Design Using Free Energy Perturbation
• New Quick Reference Sheet: Force Field Builder
• New Quick Reference Sheet: Ligand Interaction Diagram

Biologics Drug Discovery

• Release of MacroMolecular Pose Filter – Select the most plausible or relevant structural models of a macromolecular complex from a larger set of generated possibilities
• New protein descriptor – ASPmax – Added ASPmax (Maximum Average Surface Property) to our descriptor set. Used to predict the retention time of proteins in hydrophobic interaction chromatography (HIC) columns and aggregation risk
• Search and filter non-standard residues – Support for text-based searching and filtering of non-standard residues based on labels in the Name, Code, and Description columns
• Residue Lookup in the MMGBSA residue scanning panel – Quickly search and find residues to mutate
• Classification of residue scanning results – Color codes residue scanning results to designate positive, neutral or negative mutational variants based on energy score cut-offs

GUI for Quantum ESPRESSO

Product: Quantum ESPRESSO (QE) Interface

• Defect Formation Energy: Workflow solution to analyze point defects in crystals
• Options to set frequency cutoff / harmonic threshold in the Phonon DOS Viewer
• Support for TB09 density functional (command line)
• Support for rVV10-SCAN density functional (command line)
• Support for NpT ensemble in QE BOMD simulations (command line)
• (+MATSCI_NEB_MLFF) MLFF integration in NEB

MS Surface

Product: MS SurfChem

• Desorption Enumeration: WAM to open results in Adsorption Energy

Microkinetics

Product: MS Microkinetics

• Option to view selectivities and degrees of selectivity control
• Option to load/save archived MKM output
• Option to export reaction view as an image (PNG) file
• Results from individual stages made visible from the analysis panel

Optoelectronics Genetic Optimization

Product: Genetic Optimization (GA)

• Support for setting target property based on models from ML Property Prediction

Active Learning Optoelectronics

Product: Active Learning Optoelectronics

• Option to set target values excluded from optimizations

Reactivity

Product: MS Reactivity

• Nanoreactor: Option to specify separate hosts for driver and subjobs
• Nanoreactor: (+NANOREACTOR_AUTOTS) Automatic transition state search for elementary reaction network calculations via AutoTS
• Nanoreactor: Option to skip generating trajectory files
• Nanoreactor: User control over the time interval between trajectory frames
• Reaction Network Profiler: Option to refine conformer geometries using UMA (MLFF)
• Reaction Network Profiler: Option to assign stoichiometric multipliers for reactants

Transport Calculations via MD simulations

Product: MS Transport

• Ionic Conductivity: Support for MLFF

Dielectric properties

Product: MS Dielectric

• Complex Permittivity: Support for multi-component systems

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG

• CG FF Builder: Improved detection and mapping of non-isomorphic residues
• CG FF Builder: Automated particle naming scheme with chemical context
• CG FF Assignment: Up to 15x speed-up for models with a large number of particle types
• Coarse-Grained Mapping: Residue number and name retained through mapping
• Coarse-Grained Mapping: Option to import SMARTS patterns from previous use
• Speed-up for DPD simulations of up to 30% with improved cutoff margins

Complex Bilayer Builder

Product: MS Complex Bilayer Builder

• Complex Bilayer: (+COMPLEX_BILAYER_BUILDER_EXTENDED_LIPID_LIB) Expanded list of default lipids
• Complex Bilayer: Increased limit for water padding depth to 5000 Å
• Complex Bilayer: Support for custom-trained OPLS
• Membrane Analysis: (+MEMBRANE_ANALYSIS_PREP_FOR_FEP) Support for generating poseviewer formatted files compatible with FEP calculations
• Membrane Analysis: Support for applying multiple leaflet-finding algorithms

Materials Informatics

Product: MS Informatics

• Machine Learning Property: Improved panel interface for model selection
• MD Descriptors: User control over simulation system size (max # of atoms)
• MD Descriptors: Support for formulation input with path assigned to structure files
• MLFF Calculations: Option to set constraints to atomic positions
• MLFF Calculations: Support for running on GPU nodes

Formulation ML

Product: MS Formulation ML

• Formulation ML: ‘Learned Fingerprint’ as a new option to feature space
• Formulation ML: Advanced option to process (‘impute’) training set data with partially missing descriptors
• Formulation ML: Improved UI for parity plot
• Formulation ML: Support for building machine learning models using training datasets with missing chemical (SMILES) information
• Formulation ML: Target property displayed in the ‘Performance’ tab
• Formulation ML: User control over correlation threshold between features
• Formulation ML Optimization: Support for custom-ingredient descriptors
• Formulation ML Optimization: Support for multi-CPU parallelization
• Formulation ML Optimization: Option to use genetic algorithms for formulation optimization

Layered Device ML

Product: MS Layered Device ML

• OLED Device ML: User control over correlation threshold between features
• OLED Device ML: Target property displayed in the ‘Performance’ tab

MS Maestro Builders and Tools

• Adsorption Enumeration: WAM to open results in Adsorption Site Finder / Adsorption Energy
• Adsorption Site Finder: WAM to open results in Adsorption Energy
• Adsorption Enumeration: Improved organization of output structures in the Project Table
• Adsorption Site Finder: Up to 200x of speed-up for jobs using MLFF
• Clean Up Structures: Support for MLFF
• Disordered System: Option to define residue name for components
• Support for converting *.vis files to *.cub formatted files (command line)
• Polymer: Import of coupling probabilities from a CSV formatted file
• Polysaccharide: (+POLYSACCHARIDE_BUILDER) Simplified model building solution for linear-chain polysaccharides
• Single Complex: Updated list of bridging ligands
• Query Bonds: Display of polyhedra for molecular crystals
• Query Bonds: Search for and modification of non-bonded atom pairs

Classical Mechanics

• Droplet: Support for using pre-assembled droplet models
• Droplet: Support for computing contact angles with hydrate surfaces
• Elastic Constants: Support for MLFF
• (+ALLOW_OLD_FORCEFIELD_PARAMETERS) Support for running MD using OPLS4/OPLS5 parameters with backwards compatibility (2025-4 and older)
• MD Multistage: FF type for the input structure displayed in the panel
• Stress Strain: Support for MLFF
• Stress Strain: Option to use velocities from previous strain steps
• Surface Tension: Improved analysis with block averaging scheme
• Tg: (+THERMOPHYSICAL_PROPERTIES_MLFF) Support for MLFF
• Umbrella Sampling: Workflow solution to run umbrella sampling algorithm for small molecules near lipid and surfactant bilayers
• Umbrella Sampling: Displaying quantity of overlap between windows
• Viscosity: Adjusted default timestep (0.5 fs) for MLFF simulations

Quantum Mechanics

• Adsorption Energy: Option to pre-optimize structures with MLFF
• Adsorption Energy: Support for atomic positional constraints with MLFF
• Crest: (+MATSCI_CREST_QCG) CREST Quantum Cluster Growth Utility
• QM Multistage: Option to select GFN2-xTB from the list of theory
• Optoelectronic Film Properties: Display of refractive index ratio per molecular species
• Reaction Network Viewer: Comprehensive analysis viewer GUI for viewing networks created by Reaction Network Profiler and Nanoreactor

Education Content

• New Tutorial: Catalytic Selectivity Through Microkinetic Modeling
• Updated Tutorial: Defect Formation Energy Calculation
• Updated Tutorial: Nanoreactor
• Quick Reference Sheet: Clean Up Structures

Education Content

Life Science

• Introducing a new, more interactive tutorial experience, letting users intuitively click through the steps of a workflow right in the tutorial. This approach is being piloted in two tutorials.
  • Updated Tutorial: Structure-Based Virtual Screening Using Glide
  • Updated Tutorial: Introduction to Structure Preparation and Visualization
• Fully re-worked learning content on Antibody Modeling:
  The “Antibody Visualization and Modeling in BioLuminate” tutorial has been replaced by a new suite of tutorials organized in a learning path together with other helpful resources.
  • New Learning Path: Antibody Modeling
  • New Tutorial: Antibody Structure Prediction and Visualization with BioLuminate
  • New Tutorial: Humanizing Antibody Structures with BioLuminate
  • New Tutorial: Antibody – Antigen Docking with PIPER
  • New Tutorial: Improving Antibody Stability/Affinity Using MM-GBSA Residue Scanning
• New Tutorial: Generating ternary complex structures to enable rational design of targeted protein degraders
• Updated Tutorial: BACE1 Inhibitor Design Using Free Energy Perturbation
• New Quick Reference Sheet: Force Field Builder
• New Quick Reference Sheet: Ligand Interaction Diagram

Materials Science

• New Tutorial: Catalytic Selectivity Through Microkinetic Modeling
• Updated Tutorial: Defect Formation Energy Calculation
• Updated Tutorial: Nanoreactor
• Quick Reference Sheet: Clean Up Structures

LiveDesign

What’s Upcoming in 2026-1

• Design new biologics by using a new Residue Mutation tool to perform single point mutations
• Report on project status with customizable Project Dashboards
• Interact with LiveDesign using an AI Assistant, available with the LiveDesign ML add-on