Library Background

Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

  • Dynamically display measurements based on selected atoms in the Status Bar
  • Copy fragments from existing molecules in the 3D Workspace and paste them onto selected atom(s) in another molecule
  • Export movies from the Trajectory Viewer with the Workspace resolution
  • Search in the Entry List using regular expressions for greater precision. Simultaneously search for multiple structures
  • Aligned pharmacophore label font with Maestro font preferences
  • Display T-cell receptor annotations in the Structure Hierarchy
  • Automatic synchronization of data point selection in scatter plots with Project Table selections and/or Workspace inclusion
  • Display data from different groups in a single scatter plot

Force Field

  • New OPLS5 Force Field (beta): Significant improvement in the accuracy of cation-pi and ionic group interactions via the addition of limited polarizability in relative binding-FEP+ and Desmond. Available as a new option alongside the default OPLS4

Workflows & Pipelining [KNIME Extensions]

  • Supports the latest version of KNIME (v5.2)
  • The Chemistry external tool node supports a new FEP+ column type that points to fmp files read by the FEP+ reader node

Binding Site & Structure Analysis


  • More accurate identification of RNA binding sites with 89% of RNA sites in HARIBOSS set now identified as the top-ranked binding site by SiteMap, up from 69% previously (beta)
  • New SiteMap parameters to separate large pockets that are bleeding into one another or across the protein surface and identify smaller distinct sites (command line only)

Mixed Solvent MD (MxMD)

  • Support for membrane systems

Hit Identification & Virtual Screening

Ligand Preparation

Active Learning Applications

  • Enhanced diversity selection in AL-Glide through consideration of up to 3x more compounds by horizontal scaling of diversity selection
  • Significantly improved LigandML prediction throughput in AL-Glide through use of ZMQ (command line only) (beta)
  • Much faster file uploading to the DriverNode in AL-Glide (command line only) (beta)

Ligand Docking

  • Improved pose-prediction and enrichment when docking small molecules into RNA receptors with Glide (beta)

Lead Optimization


  • Support setting up Positional Restraints in RB-FEP via FEP+ panel
  • Ability to use OPLS5 for Increased RB-FEP Accuracy
  • Improved Trajectory Management allowing trajectories from multiple edges in PT

Protein FEP

  • Support of Multi-Site Mutations for Thermostability prediction

Constant pH Simulations

  • Support of Lys pKa Calculations with panel support

Solubility FEP

  • Improved Trajectory Visualization
  • Link to Best Practices document
  • Support of Force Field Builder from Web Service

FEP Protocol Builder

  • Use FEP Protocol Builder to quickly identify FEP+ model parameters that optimize FEP+ accuracy using an automated machine learning-driven workflow
    • Free researcher time by letting the FEP Protocol Builder explore parameter space to identify and visualize optimal parameters for FEP+ model performance
    • Find FEP models for challenging systems through efficient exploration of parameter space
    • Proceed with confidence to use FEP+ prospectively in your program
    • Interface to set up FEP protocol optimization calculations with automated assignment of ligands into test/training sets
    • Interface to analyze influence of parameters on FEP model performance and compare protocol performance via FEP+ correlation plots

Quantum Mechanics

  • Perform wave function stability analysis in Jaguar
  • Generate NMR chemical shifts and spectra of 19F isotope with Jaguar Spectroscopy
  • Set multiplicity automatically (multip=2) if an odd number of electrons are found in Jaguar
  • Search for atropisomers using the new script (command line only)
  • More robust and performant E-sol workflow suitable for LiveDesign and command line execution 
  • Modify level of theory and basis sets of multiple entries with a right mouse click

Medical Chemistry Design

Ligand Designer

  • New Ring Swapping workflow to optimize lead compounds by exploring alternative ring scaffolds (beta)

Biologics Drug Discovery

  • Added 430 new non-natural amino acids to the library for use in peptide design
  • Interface improvements to speed analysis of protein mutation results produced by residue scanning
  • Analyze structural ensembles such as PIPER docking results and MD trajectories  with Protein-protein interaction analysis panel (open beta)
  • New option to specify one of five numbering schemes, Chothia, Kabat, IMGT, Enhanced Chothia or AHo, when performing antibody structure alignment using the script

Materials Science

GUI for Quantum ESPRESSO

Product: Quantum ESPRESSO (QE) Interface

  • Input for magnetization from structure data (command line)
  • Results viewer for solid state NMR spectra
  • NEB Convergence Monitor: Display of relative / activation energies
  • Automatic shift of K-point grids for improved convergence
  • Option to compute and visualize potential surfaces in the workspace
  • Phonon Density of States Viewer: Support for dielectric constant
  • Speed-up of NEB calculations with smart management of wave function data

KMC Charge Mobility

Product: MS Mobility

  • Compute KMC Charge Mobility: Charge transfer computed based on center-of-mass distances

Materials Informatics  

Product: MS Informatics

  • Formulation ML: Support for input data with missing component names / SMILES
  • Formulation ML: Support for Set2Set and graph-based models and descriptors added
  • Formulation ML: Option to remove highly-correlated descriptors (command line)
  • Formulation ML: Option to control the training set size
  • Formulation ML: Support for classification mode
  • Formulation ML: Feature-importance analysis based on Shapley additive explanations (SHAP)
  • Machine Learning Property: Improvements in prediction models available for download
  • Machine Learning Property: Prediction of oxidation and reduction potentials
  • MD Descriptors: Support for formulations-focused descriptors

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG

  • Coarse-Grained Force Field Builder: Automatically map atomistic systems to Martini particles (command line)
  • Coarse-Grained Force Field Builder: Fit Martini parameters (command line)


Product: MS Reactivity

  • Nanoreactor: Improved default settings
  • Nanoreactor: Speed-up of xTB frequency calculations
  • Nanoreactor: Improved deduplication algorithm for products
  • Nanoreactor: Improved parallelization algorithm
  • Nanoreactor: Option to remove high-energy products
  • Nanoreactor: xTB free energy used to rank-order products
  • Auto Reaction Workflow: Prevention of excessive equilibrium constant calculations from permutations


Product: MS Microkinetics

  • Microkinetic Modeling: Support for the use of analytical Jacobian
  • Microkinetic Modeling: Option to specify collision factor
  • Microkinetic Modeling: Results returned for cases that did not reach a steady state
  • Microkinetic Modeling: Option to list chemical equations from the input reaction network

Reactive Interface Simulator

Product: MS RIS

  • Solid Electrolyte Interphase: Reaction-template based solution for dynamic simulations of materials systems near battery electrodes

MS Maestro Builders and Tools

  • Density Profile: Visualization of density isosurfaces
  • Complex Builders: Option to clean up geometry using xTB
  • Semicrystalline Polymer: Support for polyvinyl alcohol (PVA)
  • Solvate System: Protocol to manage output with more than 2M atoms
  • Structured Liquid: Protocol to manage output with more than 2M atoms
  • Structured Liquid: Improved and expanded built-in lipid library

Classical Mechanics

  • Thermal Conductivity: Solution to predict thermal conductivity of solids

Quantum Mechanics

  • Adsorption Enumeration: Improved algorithm to define surface atoms
  • Adsorption Enumeration: Heavy-atom filter for reactive atoms
  • Amorphous NMR: Isosurface data available from QM calculations


Education Content

Life Science

  • New Tutorial: Ligand Binding Pose Prediction for FEP+ using Core-Constrained Docking (NEW)
  • New Tutorial: Ligand-Based Virtual Screening Using Phase (large-scale rework from the ground up)

Materials Science

  • New Tutorial: NMR Spectra Prediction
  • New Tutorial: Thermal Conductivity
  • New Tutorial: Solid Electrolyte Interphase Calculations
  • New Tutorial: Building a Semicrystalline Polymer
  • Updated Tutorial: Machine Learning for Formulations
  • Updated Tutorial: Update tutorials for switch to RDKit (affects multiple tutorials)


What’s New in 2024-2

  • Biologics Support
    • Upload peptides, monoclonal antibodies, bispecific antibodies, Fab, Fab2, Fv, DNA, and RNA
    • Biologics automatically get broken down into their component chains and can be visualized in composite rows
    • View and align sequences in a sequence viewer
    • Upload experimental data and metadata
    • View 3D model results and apply styling
    • View an antibody’s hierarchy in 3D visualizer and select and style at the full biologic, domain (ex: VH, CH1), subdomain (ex: HCDR3), or residue level
    • Full support within Models, MPOs, Formulas, Freeform columns, Forms, Tile View, Filters, and Search
    • Search and Filter for Biologics based on the properties of their chains
  • Updated User Management in the Admin Panel
    • See and update all Users’ ACL and details on single page
    • Quickly add and remove multiple users at once
    • Bulk update users’ roles, projects, and license status
    • Create a project and add users, groups, admins to the project on single page
    • Project and Group details pages give clearer statistics on users and access control flow
    • Choose to send or resend a welcome email on updates
    • Sync users between LiveDesign and externally hosted, read-only LDAP, to pre-populate users before their first login
  • One-click to view 3D model results in Maestro: Click a link in a 3D model cell to automatically open Maestro and view the result. Note that this only works in Windows, using Maestro version 24-2; Mac and Linux support are forthcoming in Maestro’s 24-3 release
  • Structure Groupings for the 3D Visualizer
    • Group any number of 3D outputs in a single structure group, beyond the historic Ligand + Protein combination
    • Add custom group titles to change the displayed column title
    • View multiple ligand poses or protein poses in the 3D visualizer content panel
  • Control Display styles in Ligand Designer
    • Style selected atoms, resides, and chains from a new toolbar within the 3D canvas in Ligand Designer
    • Apply custom styling to Proteins and Ligands within a Ligand Designer session
    • Use 3D tools within Ligand Designer, such as export, zoom, and screenshot
  • Complex Filters: Combine filter conditions using AND or OR logical operators
  • Published Limited Assay Columns: Publish limited assay columns so they appear in the Data & Columns tree, and are available for use in published column-as-parameter models, MPOs, and published formulas
  • Pinned Rows: Click a button on a row or a Tile to “pin” the compound to the top of the LiveReport
  • UX Improvements
    • Forms
      • Toggle the number of tiles to show in each row in a Kanban widget
      • Freeform column cells now render larger editing areas in the Matrix Widget when the cells are small
    • Plots
      • Plot can’t be created or edited in read only LRs
      • Delete plots directly from the visualize panel, without opening them first
      • Search for columns in plot axis selection dropdowns
    • Spreadsheet interactions
      • Freeze multiple columns at once via the column menu
      • Double-click on a Freeform column cell to edit its value
      • The Run button for click-to-run models is now displayed as a solid color
      • Right-click on a LiveReport tab to reveal the LiveReport menu
    • 3D Visualizer
      • Downloaded files from the 3D visualizer now show the same labels in Desktop PyMOL instead of hashed values
      • Binding Site Interaction Map is turned off by default when opening a Ligand Designer session
    • Miscellaneous 
      • The login page now allows submitting either Single sign-on or username + password credentials
      • Export the Tile View configuration to PPTX using LDClient
      • Archive a model without fixing errors in the model settings
      • The Job Manager gadget table now resizes as the tool is resized
      • Click Help icons in the Create Freeform Column dialog, Create Formula column dialog, and the Define New Multi-Parameter Optimization dialogs to navigate directly to the user manual
      • Click an icon within the Data & Columns Tree LiveReport tab to scroll to the column in the LiveReport
      • Drag and add multiple scaffolds to the R-group enumeration scaffold sketcher
    • TaskEngine workers now scale up when the number of submitted jobs increases
    • The Schrodinger Suite python method “from schrodinger.structure import SDReader” has been deprecated, and scripts should instead call “from schrodinger.structure import StructureReader”

What’s Been Fixed

  • The Landing Page Overview would occasionally fail to show the most recently added compounds, and now correctly shows them
  • Columns that are added to LiveDesign via the Data Integrator are now set to the correct datatype
  • LiveReports no longer show duplicate rows for a Real and a Virtual after uploading experimental data via ACAS
  • LiveDesign now correctly opens the most recently opened Project and LiveReport after logging in
  • Users can now log out of LiveDesign when Single Sign-On is enabled
  • Freeform column picklist options order would previously change, and is now maintained according to the configuration set within the Edit Freeform Column dialog
  • Security
    • CVE-2023-44487 has been patched
  • Admin Panel
    • Uploading a file in the Admin Panel now works correctly when the filename is identical to the file that is being replaced
    • The Last Modified Date shown in the Admin Panel’s Protocol page and Protocol List page now correctly updates for all changes to the Protocol
    • The “Last Login” date field within the Admin Panel’s User page now correctly updates
  • File Exports
    • Enhanced stereo labels now show in all images in PowerPoint exports
    • Exporting Tile View to PowerPoint now correctly warns the user when attempting to show more than 8 compounds per slide
  • Forms
    • Tiles now render correctly in Tile View widgets, when the Tile View widget is in the same container as another widget
    • Tooltips in Tile View would previously get frozen after displaying R-group decomposition results, and how correctly show data for each cell
    • Tile view tooltips now render correctly-sized R-groups when hovering over a R-group decomposition cell
    • The Forms Entity Image widget now correctly shows the ID of the entity
    • Forms drilldown from a row-per-compound widget to a row-per-pose widget now correctly shows the poses only for the selected compound(s)
    • The Forms Matrix widget now shows the entity image for Generic Entities
  • LDClient
    • A ‘parent_row_key’ has been added to the LDClient RowInfo object within LiveReportResultsMetadata, which identifies which rows are child composite rows in the LiveReport
    • LDClient ldclient.LDClient.refresh_db_constants method and the AboutInfo remaining_read_only_licenses_count field have been deprecated and removed
    • LDClient now correctly returns a LiveReport’s filters, when the filters include a substructure query
    • LDClient’s ModelTemplateVarType enum now includes LIST_INPUT and RDKIT_MOL
    • Scripts calling LDClient occasionally needed to execute a LiveReport, and include a manually programmed sleep to get results. LDClient now includes a method mutate_then_wait, which allows code to wait on actions to be completed before continuing (such as adding rows to a LiveReport)
  • Ligand Designer
    • Ligand name shows up correctly in Ligand Designer, when the LiveReport is in row-per-pose mode
    • Grid files can now be changed for existing Ligand Designer configurations in the Admin Panel
  • Maestro Export
    • LiveReport exports from LiveDesign to Maestro now work correctly when two Real compounds are linked to the same Virtual compound
    • Maestro exports to LiveDesign with published data are now faster
  • Matched Molecular Pairs
    • Previously calculated Matched Molecular Pair analyses have been deleted due to a backwards-incompatible Python library upgrade, and must be re-run
    • The Matched Molecular Pairs tool now shows an error message when large LiveReports fail to complete the matched pairs computation
  • Spreadsheet Interactions
    • Searching by substructure in the active LiveReport will now deselect existing row selections, and select the matching substructures
    • Compound orientations in the sketcher are now saved when adding the compound to a LiveReport, using a scaffold in R-group decompositions, using a scaffold for compound alignment, and using compounds in enumeration
    • The row-per-model toggle is no longer obscured when the visualizer panel is open
    • Searching a LiveReport via the magnifying glass now correctly navigates to the first matching string
    • Calculated properties that appear below the sketcher now truncate long column names to avoid an overlap with the calculated value
    • Attempting to recalculate an archived model would show flashing cells, as if the calculation has been started (despite no calculating being started), and will now show an error message
    • Searching for metadata within assay columns’ Edit Tooltip Content now correctly filters content that does not match the query
    • Copy and Paste coloring rules for R-group decomposition columns
    • Copying a compound into the sketcher via the row menu’s “Use in → Design/Search Sketcher” option will now correctly overwrite any compound within the sketcher
    • Importing a compound multiple times to the sketcher using its ID will now correctly show the compound’s structure
  • Plots
    • Box plots now show a border around selected outlier data points to make them more noticable
    • Scatter plot tooltips now show assay datapoint operators, such as ‘greater than’ and ‘less than’
Release 2024-1

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