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Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

  • Create and share custom visualization Presets  [2022-4]
  • Added support to mutate DNA/RNA to standard nucleobases  [2022-4]
  • New Workflow Action Menu to guide to next steps for Plot Rigid/Relaxed scans [2022-4]
  • First full release of the new 2D sketcher [2022-4]
  • Get Going with Maestro Video Series added to Documentation [2022-4]

Workflows & Pipelining [KNIME Extensions]

  • Includes the latest version of KNIME (v4.6.1) [2022-4]
  • The number of matches can now be controlled in the Phase screening node [2022-4]

In LiveDesign:

  • When deploying a model the suitable KNIME protocol is chosen automatically and the latest version of the protocol uploaded [2022-4]
  • Distribution of calculations is controlled from the model admin page [2022-4]
  • Model changes from the LiveDesign Admin page can be preserved when overwriting an existing model [2022-4]
  • A new administration node to move, archive and unarchive models [2022-4]

Target Validation & Structure Enablement

Protein Preparation

  • Significant speedup when opening the Protein Preparation Workflow interface on Windows [2022-4]
  • Reduced verbosity of Protein Preparation Workflow log file by limiting irrelevant CCD bond assignment error notices [2022-4]
  • Protein Reliability Report will generate TEST reflections on-the-fly, if not available in provided .cv file, and report RSCC values [2022-4]
  • Updated PROPKA to (latest) version 3.4 [2022-4]

Protein X-Ray Refinement

  • Introduction of GlideXtal command line tool for automatic ligand fitting in crystallographic electron density maps [2022-4]
  • PrimeX minimization is able to use structure factors in CIF format [2022-4]
  • In Phenix/OPLS can now remove all entities clashing with crystal mates [2022-4]
  • Phenix/OPLS is more robust to missing atoms in standard residues [2022-4]

Cryo-EM Model Refinement

  • Beta GlideEM interface for ligand placement into cryo-electron density maps [2022-4]
  • GlideEM now accepts gzipped (CCP4, MRC, MAP) files as input [2022-4]

Multiple Sequence Viewer/Editor

  • Beta release of Protein Family Alignment and Annotation [2022-4]
    • A new category named ‘Family Feature Calculation’ located in the ‘Other Tasks’
    • Menu exposes protein family alignment and annotation
    • Supports kinase and GPCR Alignments
    • Supports annotation of GPCR regions
  • Dendrogram hover tooltip to display distance information [2022-4]


  • Membrane-bound IFD-MD tutorial [2022-4]
  • Covalent ligand IFD-MD tutorial [2022-4]


  • Show user-friendly message when undefined stereochemical centers are introduced [2022-4]
  • Improved usability of FEP+ group panel to manage protonation and tautomeric states ensemble – for more accurate ΔΔG predictions [2022-4]

Constant pH Simulations (Beta)

  • Improved usability of constant pH simulations for protein pKa calculations with friendly outputs [2022-4]


  • Added MACCs keys for ligand featurization in DeepAutoQSAR [2022-4]
  • Include ElasticNetCV model (strongly l1/l2 regularized linear regression) in DeepAutoQSAR hyper-parameter optimization [2022-4]
  • New DeepAutoQSAR command line utility for greater ease-of-use [2022-4]

Desmond Molecular Dynamics

  • In Trajectory Plots view Ramachandran plot of Protein Residues [2022-4]

Empirical and QM-based pKa Prediction

  • Initial release of Epik 7, a new machine learning based application for fast pKa value and protonation state prediction [2022-4]
    • Epik 7 can also produce a plot giving the populations of states as a function of pH

Solubility FEP (Beta)

  • Option to show solubility results in logS unit [2022-4]

Quantum Mechanics

  • Calculate ESP charges for excited states under the TDDFT/TDA approximation [2022-4]
  • Complete calculations faster with parallel Jaguar calculations on Windows [2022-4]
  • New Workflow Action Menu to guide to next steps for Plot Rigid/Relaxed scans [2022-4]
  • Over 80 examples of Jaguar input files in documentation [2022-4]

Semi-Empirical Quantum Mechanics

  • GFN2-xTB method now available in the Semiempirical Module panel [2022-4]

Biologics Drug Discovery

  • To improve protein linker design, the loop database was updated to a new version specifically intended for interdomain linker design [2022-4]
  • To expand chemical liability detection, Asp isomerization pattern and free cysteine detection were added to the Reactive Residues interface [2022-4]
  • New command-line script for running Protein Interaction Analysis with the ability to export results to csv format [2022-4]
  • First full release of Protein Descriptors interface which now supports .mae and .maegz files containing multiple structures [2022-4]
  • Copy-paste sequences into Antibody Structure Prediction interface under new “Enter new sequence” option [2022-4]
  • Reuse the same input csv file format for batch homology modeling in Antibody Structure Prediction when running from the command line or Maestro [2022-4]
  • Added support for ‘keep glycan’ option in Antibody Structure Prediction during batch modeling [2022-4]
  • Cysteine scanning panel for disulfide design now supports remote job submission which is useful for running large jobs e.g. using when MD trajectory as input [2022-4]
  • Added “Antibody-Antigen” to Interactions scope dropdown [2022-4]
  • Get Going with BioLuminate Video Series added to Documentation [2022-4]

Materials Science

GUI for Quantum ESPRESSO

  • Quantum ESPRESSO GUI: Option to hide selected atoms [2022-4]
  • Quantum ESPRESSO GUI: Upgraded NEB UI for improved UX [2022-4]
  • Quantum ESPRESSO: Endpoints saved for NEB mae files at each iteration [2022-4]
  • Quantum ESPRESSO: Reduced file size for custom saved NEB setups [2022-4]
  • Quantum ESPRESSO: Use of automatic parallelization with GUI support [2022-4]
  • Quantum ESPRESSO: -save_failures option for driver (command line) [2022-4]
  • Quantum ESPRESSO: -last_only option for qe2mae tool to save the final structure only  (command line) [2022-4]
  • Quantum ESPRESSO: HUBBARD options enabled in input *.cfg (command line) [2022-4]
  • Quantum ESPRESSO: Automatic restart for long AIMD simulations [2022-4]
  • Quantum ESPRESSO: Support for cell volume relaxation [2022-4]

Molecular Dynamics

  • Viscosity: ”,” used as the delimiter in CSV output for Einstein-Helfand analysis [2022-4]

Materials Informatics

  • Machine Learning Property: Pre-built, validated machine learning models for a selective list of materials properties [2022-4]
  • Molecular Descriptors: Report of semiempirical HOMO-LUMO gap [2022-4]
  • Molecular Descriptors: Support for plotting molecular orbitals [2022-4]

Coarse-Grained (CG) Molecular Dynamics

  • Support for Ewald sums with Martini force field [2022-4]
  • CG FF Builder: Option to export the viewer data to CSV [2022-4]
  • CG FF Builder: Support for the use of existing trajectory [2022-4]
  • Map Atoms to Particles: Option to map selected atoms from the input structure [2022-4]

Penetrant Loading Simulation

  • Penetrant Loading: Robust handling of GCMC water models [2022-4]
  • Penetrant Loading: Visualization of periodic unit cell for the output structures [2022-4]

MS Maestro User Interface

  • Resized Trajectory Analysis task frame in Maestro for better user experience [2022-4]

MS Maestro Builders and Tools

  • Complex Builder: Expansion of ligand library [2022-4]
  • Disordered System: Option to generate cells with different numbers of molecules [2022-4]
  • Elemental Enumeration: Jobs launched to queue instead of running interactively [2022-4]
  • Manipulate Cell: Option to translate within -0.5 and 0.5 of the fractional coordinate [2022-4]
  • Manipulate Cell: Support for change of lattice dimensions without FF retyping [2022-4]
  • Query Bonds: Option to export output to CSV [2022-4]
  • Semicrystalline Polymer: Option to use existing crystal (command line) [2022-4]
  • Semicrystalline Polymer: Reporting percentage of crystallinity [2022-4]
  • Semicrystalline Polymer: Speed-up for building with polymer models [2022-4]

Classical Mechanics

  • MD Multistage: Improved estimation of timestep for Martini systems [2022-4]
  • MD Multistage: Option to concatenate stages together for speed-up [2022-4]
  • MD Multistage: Built-in Martini relaxation protocol suitable for NVT ensemble [2022-4]
  • MD Multistage: Option to only write out selected molecules to trajectories (command line) [2022-4]
  • Stress Strain: Output CSV updated at each new data point [2022-4]
  • Thermophysical Properties: Support for Parrinello-Rahman barostat (command line) [2022-4]

Quantum Mechanics

  • Band Shape: Option to add/select implicit solvent [2022-4]
  • Organometallic Conformational Search: Option to select conformers after QM calculations (command line) [2022-4]
  • Organometallic Conformational Search: Support for custom MacroModel COM files (command line) [2022-4]
  • Organometallic Conformational Search: Support for MOPAC (command line) [2022-4]

Education Content

  • Get Going with Materials Science Maestro Video Series added to Documentation [2022-4]
  • Quick Reference Sheets available from both Documentation and Training webpages [2022-4]
  • New Tutorial: Evaporation [2022-4]
  • New Tutorial: Machine Learning Property Prediction [2022-4]
  • Updated Tutorial: Polymer Electrolyte Analysis [2022-4]
  • Updated Tutorial: Computing Atomic Charges [2022-4]
  • Updated Tutorial: Activation Energies for Reactivity in Solids and on Surfaces [2022-4]
  • Updated Tutorial: Organometallic Complexes [2022-4]


What’s new in LiveDesign 2022-4

  • The number of logins is enforced by a license limit: Users who attempt to log in after the number of available seats have been assigned will be denied access to LiveDesign
  • Admins can forcibly log out users: Users can be forcibly logged out by removing their assigned Roles, or by specifying a specific username
  • File Import Receipt: Receive feedback on file imports when the file contains errors, and instructions on how to correct the errors
  • Sketcher Improvements:
    • Implicit mode sketcher: Quickly switch between editing compounds and selecting a subset of the compound, by clicking directly on the select tools and draw tools
    • Delete an atom by hovering over it and pressing the Backspace key on the keyboard
  • Setting a protocol’s parameter to “Set Default” in the admin panel changes all existing models’ parameter to “Set Fixed”
  • Interaction Surface within LigandDesigner: view the interaction surface to determine available growth space within a binding pocket
  • Copying a single compound from the spreadsheet can be copied in a Mol v3000 format: a server wide setting permits copying a single molecule as either Extended SMILES or Mol v3000. Selecting and copying multiple compounds as once will copy the compounds using a SMILES format
  • Freeform column picklist options can be reordered: Editing a Freeform column definition permits reordering the picklist options
  • UI Improvements
    • View more tiles on screen in Tile View, which has a much smaller tile size limit
    • View more data in a spreadsheet cell; the “More Available…” message within spreadsheet cells has been replaced with a gradient to indicate additional data is in the cell
    • Users can use Ctrl-Click to easily display results from additional 3D models in the 3D visualizer.
    • Exported compound structure images will now include stereochemistry labels if these are turned on in the spreadsheet.

What’s Been Fixed

  • Model columns can now be sorted and filtered when the cell contains both blank values and numeric or string values. Sorting will use the first non-empty value in the cell.
  • Advanced searches with multiple Freeform column conditions return the same results even if the condition order is changed
  • Compound images no longer show large atom labels when clicking on them within the main spreadsheet
  • Project admins can edit all formulas within their projects
  • Pinned plot tooltips in the visualize panel will reappear even after switching to another plot or another LiveReport
  • Deleted LiveReports cannot be reopened by navigating directly to the LiveReport’s URL
  • Pinned plot tooltips in forms update the connecting line when the view is resized
  • Pasting multiple values into Filters will, once again, attempt to automatically identify the delimiter, or present an option to select the delimiter, by which to separate values.
  • The LiveReport Manager dialog no longer obscures the last LiveReport with a horizontal scroll bar
  • Bond angles for attachment points and carbon atoms from R-group decompositions are now displayed as angles of less than 180 degrees, while before they were displayed at a 180 degree angle
  • LiveReports with 3D model returns no longer show a red error bar after opening
  • Commons-text has been upgraded to patch security vulnerability CVE-2022-42889
  • The 3D visualizer uses the high performance GPU on client computers to avoid crashes
  • Formula results no longer disappear from the spreadsheet when columns used in the formula are hidden in the LiveReport
  • The matched molecular pairs tool no longer fails to parse chiral compounds represented in an Extended SMILES format
  • Error messages no longer sporadically appear when models are updated and saved in the Admin Panel
Release 2022-3

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