Schrodinger Suites 2025-3

Platform Environment

Maestro Graphical Interface
- Hovering the cursor over an atom in the Workspace now simultaneously highlights its corresponding row in the Project Table and displays its row number in the Status Bar
- Improved defaults to “Get PDB Dialog” to auto display 2Fo-Fc diffraction data and auto set isocontours in EM maps to the Author recommendation
- Redesigned 2D Viewer Export with dedicated options dialog to control image size and support for high-quality SVG format for both single structures and HTML grids
- New Maestro Assistant (beta) – An AI-powered conversational interface providing context-aware help via the Schrödinger Knowledge Bot and enabling natural language styling command execution within the 3D workspace
Force Field
- Updated FFBuilder default reference method to the MPNICE potential
. Roughly 5x faster for typical chemistries
. 20x faster for boron, bromine, iodine and silicon containing compounds

Target Validation & Structure Enablement

Protein Preparation
- Protein Preparation Wizard interactive jobs now save temporary files under a named folder in the Maestro working directory
Protein X-Ray Refinement
- Improved defaults to “Get PDB Dialog” to auto display 2Fo-Fc diffraction data and auto set isocontours in EM maps to the Author recommendation
- Redesigned GlideMap panel to dock ligands into maps generated from X-ray data by GlideXtal
Cryo-EM Model Refinement
- Redesigned GlideMap panel replaces the GlideEM panel with more granular options for fitting small molecule ligands into cryo-EM density maps
IFD-MD
- New Template Ligand Finder for ligand-binding mode prediction and cryptic binding site identification (Beta): Rapidly identify and visualize homologous proteins based on both protein and ligand similarity to uncover potential template ligands as references for IFD-MD

Binding Site & Structure Analysis

Mixed Solvent MD (MxMD)
Enhanced cryptic binding site identification with updated in silico workflow (Beta): New workflow combining mixed solvent molecular dynamics (MxMD) with SiteMap to reliably reveal and detect cryptic binding sites

Hit Identification & Virtual Screening

Docking
- Optimized Glide which is nearly 2x faster than Glide is now the default method
- Revamp of the Glide WS MMGBSA correction

Ligand Preparation

Macrocycles
- Add command-line options to restrain cis/trans isomerism during alignment with tug_align.py
- Add a command-line option to tug_align.py to control MCS search algorithm timeout
- Small performance improvements to PrimeMCS
ABFEP
- Automatic membrane placement for AB-FEP simulations

Lead Optimization

FEP+
- New Settings interface that replaces the Advanced Options interface for more intuitive and easy simulation set up
- Clear predictions for RB-FEP edges
- Similarity Score column displayed in the analysis tab
- Batch delete and download multiple jobs with enhanced usability of the ‘Web Services Jobs Table’ panel
- Extend Atom Mapping to matched R-groups
Constant pH Simulations
- Improved panel usability and layout
- Added support to run constant pH simulations via Web Services
FEP Protocol Builder
- Roughly 2X speedup in workflow through improved defaults
- Improved accuracy in generated FEP+ maps through exploration and scoring of submaps with Louvian clustering. Alternatively, users can input desired submaps
- New cost-optimal option using Pareto Selection of FEP-PB Models to generate the best value protocols
- Improved prediction accuracy of generated maps through FEP+ Groups support, where ligands with different protonation, tautomeric, and conformational forms will be grouped, enabling FEP Group corrections to be applied
Quantum Mechanics
- Predict Ames toxicity via a QM-based workflow following Leach et al. (2009)
- X-ray emission spectroscopy (XES) prediction is now available (command line only)
- Implemented nine new double hybrid functionals with RI-MP2: B2-PLYP, B2GP-PLYP, DSD-BLYP, DSD-PBEP86, PWPB95, B2K-PLYP, B2T-PLYP, DSD-PBEB95, MPW2-PLYP
- Wave function stability analysis automatically corrects SCF instabilities leading to a more stable wave function
- Predict Nucleus-Independent Chemical Shifts (NICS) with new workflow
- Optical rotation as a function of wavelength
- Employ MLFFs (machine learning force fields) by setting Level of Theory option
- MPNICE now supported in all Jaguar workflows that have supported use of QRNN
Biologics Drug Discovery
- Easily specify mutational variants to be modeled in MMGBSA Residue Scanning by uploading an input FASTA file
- Load, analyze and visualize in the MSV desired mutations specified in the MMGBSA Residue Scanning Panel by newly available export of variants to a FASTA file
- Macromolecular Pose Filtering supports multi-chain ligands when filtering based on data obtained from Hydrogen-Deuterium Exchange (HDX) experiments
- Added a predefined selection for the Vα-Vβ interface, located under the TCR Regions menu, to enable one-click selection of this key binding region
- New T cell receptor (TCR)-specific presets

Materials Science

GUI for Quantum ESPRESSO
Product: Quantum ESPRESSO (QE) Interface
- Defect Correction: (+DEFECT_FORMATION_ENERGY) Formation energy computed in the panel
- Finite displacement method for phonons (command line)
- Increased number of iterations and cycles for default setup
- Support for GBRV pseudopotentials by default
MS Surface
Product: MS SurfChem
- Desorption Enumeration: (+ASSOCIATIVE_DESORPTION) Option for associative desorption
Microkinetics
Product: MS Microkinetics
- Calculation of selectivity from Catalytic Reaction Analysis (command line)
Reactivity
Product: MS Reactivity
- Reaction Network Profiler: Support for Garza solvation entropy partition functions (command line)
- Nanoreactor: Improvements to elementary reaction network algorithms
KMC Charge Mobility
Product: MS Mobility
- Option to compute field-dependent mobility based on charge diffusion (command line)
Dielectric properties
Product: MS Dielectric
- Complex Permittivity: Option to apply custom fitting parameters
- Complex Permittivity: Display of predictions from multiple fits
- Complex Permittivity: Option to input a pre-equilibrated structure
- Complex Permittivity: Improved speed from KWW parameter calculations
Reactive Interface Simulator
Product: MS RIS
- Solid Electrolyte Interphase: Support for custom reactions that modify bond orders (command line)
- Solid Electrolyte Interphase: Improved algorithm to track unpaired electrons
Crystal Structure Prediction
Product: Crystal Structure Prediction
- Crystal Structure Prediction: Simplified UI for improved UX
- Crystal Structure Prediction: All space groups shown in Advanced Settings
Advanced Force Field Applications
Product: MS FF Applications
- Machine learning force field support in QM and MD panels
Transport Calculations via MD simulations
Product: MS Transport
- Diffusion: Support for GPU calculations on driver host
- Ionic Conductivity: (+IONIC_CONDUCTIVITY) Workflow solution to predict ionic conductivity in liquids
- Thin Plane Shear: (+PLANE_SHEAR_VELOCITY_PROFILE) Reduced noise in velocity profile
- Thin Plane Shear: (+PLANE_SHEAR_VELOCITY_PROFILE) Direct calculation of viscosity velocity profile
- Thin Plane Shear: Improved control of shear area to avoid drift of slabs
Coarse-Grained (CG) Molecular Dynamics
Product: MS CG
- Speed up for assignment of the coarse-grained force fields for large systems
- Coarse-grained Mapping: GUI panel for automatic mapping of CG structures
- CG FF Builder: Automated addition of antifreeze water for MARTINI mapping
- CG FF Builder: (+CGFF_BUILDER_MARTINI_NPT) Support for NPT ensemble during the fitting of MARTINI force field parameters
- CG FF Builder: Support for encrypted force field parameters
- CG FF Builder: Support for loading output from CG Mapping as input
Materials Informatics
Product: MS Informatics
- Machine Learning Property: Tooltip to visualize the training set chemical space
- MD Descriptors: Automated setup for label and number of components from input CSV
Formulation ML
Product: MS Formulation ML
- Support for the description of ingredients without SMILES strings
- Formulation ML: Visualization of model performance from the GUI
- Formulation ML: Option to export feature importance to CSV
- Formulation ML: Option to compute feature importance during training
- ML Model Manager: GUI for management of model and version information
Layered Device ML
Product: MS Layered Device ML
- OLED Device ML: Support for classification models
MS Maestro Builders and Tools
- Adsorption Enumeration: Improved adsorption for sterically hindered atoms
- Adsorption Enumeration: De-duplication for molecular adsorption
- Complex Builder: Title suggestions for sketched ligands based on IUPAC name
- Complex Builder: Build dimeric organometallic complexes
- Disordered System: Speed-up for snap-to-grid and amorphous modes
- Disordered System: Support for MLFF
- Meta Workflows: Support for MLFF
- Polymer: Setup for angles on coarse-grained polymer models
Classical Mechanics
- Complex Bilayer: (+COMPLEX_BILAYER_BUILDER) Model building solution for complex protein membrane systems
- Diffusion: Support for MLFF
- Polymer Crosslink: Speed up with improved crosslinking algorithms
- Electrolyte Analysis: Option to plot density distribution isosurface
- MD Multistage: Preset relaxation protocol for stiff polymers
- MD Multistage: Preset relaxation protocol to aid convergence in OPLS5
- MD Multistage: Option to choose electric field units
- MD Multistage: Option to view steps from the preset relaxation protocols
- MD Multistage: Support for MLFF
- Molecular Deposition: Support for MLFF
- Polymer Chain Analysis: Improved speed on searching for backbone atoms
- Prepare for MD: Support for MLFF
- Radial Distribution Function panel restored for user access
- Visualize Restraints: Tool to show restraints in systems for MD simulations
Quantum Mechanics
- Adsorption Energy: Support for MLFF
- Beta Elimination: Support for MLFF
- Bond and Ligand Dissociation: Molecular formulas printed for fragments
- Nanoreactor: Support for MLFF
- Optoelectronic Film Properties: Option to calculate the reorganization energies for ISC/RISC
- Optoelectronic Film Properties: Option to plot the distribution of singlet-triplet splittings for ISC/RISC in the viewer panel
- Probe Grid Scan: Support for MLFF
- Reaction Energetics Enumeration: Support for MLFF
- Reaction Network Profiler: Support for MLFF

Materials Science

Life Science
- New Tutorial: Preparing Nucleic Acid Structures
- New Tutorial: Structure Visualization and Interaction Analysis in Nucleic Acids
- New Tutorial: Analyzing Binding Sites of Nucleic Acids with SiteMap
- New Tutorial: Small Molecule – Oligonucleotide Docking with Glide
- New Tutorial: Forming RNA – Ligand Interactions with Ligand Designer
- New Tutorial: Potency Predictions for RNA-Binding Small Molecules Using RB-FEP
- New Tutorial: Predicting Drug Residence Times from Unbinding Kinetics Simulations
- New Learning Path: Oligonucleotide Modeling
- Quick Reference Sheet: GlideMap
Materials Science
- New Tutorial: Machine Learning Force Field
- Updated Tutorial: Nanoreactor
- Updated Tutorial: Organometallic Complexes
- Quick Reference Sheet: MLFF Calculations
- Quick Reference Sheet: ML Model Manager
- Quick Reference Sheet: Coarse-Grained Mapping
- Quick Reference Sheet: Visualize Restraints
- Quick Reference Sheet: Welcome Screen
Documentation Content
- Licensing information displayed in panel help documentation
- Materials Science Panel Explorer: Filter for panels that support MLFF

LiveDesign

What’s Upcoming in 2025-3
- Upload 3D files into a Freeform column cell and view the structure in the 3D visualizer: View and run parameterizable models on custom 3D inputs
- Overwrite and append file-uploaded data on Biologics: Track and register entities while sequencing