New Features

Format: Dec 2023
Format: Dec 2023

Platform Environment

Maestro Graphical Interface

  • Improved functionality and enhanced usability in the new embedded Workspace Sequence Viewer [2023-4]
  • Improved Scatter Plot capabilities: An updated charting tool provides a more intuitive interface, interactive features for data exploration, and extensive customization options for generating scatter plots [2023-4]
  • New Lasso Selection: Draw a freeform selection path with superior precision around specific atoms or regions compared to Marquee Selection [2023-4]
  • New 3D Builder behavior preference to automatically minimize newly added fragments [2023-4]
  • Redesigned ‘Find Toolbar’ boasts an improved user interface with new functionalities such as sequence search and enhanced "Search by SMARTS" with access to the Sketcher [2023-4]
  • Added support for Nonstandard Amino Acids in the 3D Builder [2023-4]
  • Improved user interface for several Project Table dialogs [2023-4]:
    • Combine Properties 
    • Copy Property 
    • Delete Properties 
    • Clear Values 
  • Added menu option to move selected entries to the top or end of their current group [2023-4]
  • Enhanced surface visuals through texture mapping, utilizing per-vertex texture coordinates to enrich detail and color vibrancy [2023-4]
  • mmCIF files (.cif) are now treated the same way as PDB files (.pdb) upon import into Maestro, with atoms automatically colored by element for improved visualization [2023-4]

Force Field

  • FFBuilder now uses the QRNN-TB neural network potential as its default reference method. Typical FFBuilder jobs run 3-5X faster [2023-4]

Workflows & Pipelining [KNIME Extensions]

  • LiveDesign connection node supports Single Sign-On and reconnection to hosts running different LiveDesign versions [2023-4]
  • LiveDesign connection node can be connected to the Upload as LiveDesign node [2023-4]
  • LiveDesign settings are stored for several hosts as profiles in KNIME preferences panel [2023-4]


Lead Optimization

Ligand alignment

Improved performance of macrocycle alignment for cis- and trans-bond containing macrocycles [2023-4]


  • Improved analysis of multiple physical properties in FEP+ panel [2023-4]
    • Small Molecule FEP
      • Relative Solvation
      • Relative Binding
    • Solubility FEP: 
      • Hydration
      • Dissolution
    • Protein FEP:
      • Selectivity
      • Thermostability
  • Additional settings in Advanced Options Panel [2023-4]
    • Equilibration time
    • Simulation time is split into solvent/complex/vacuum 
  • Improved accessibility for submitting jobs to web services [2023-4] 

Constant pH Simulations

  • Trajectory Player: Improvements to the Lambda Dynamics [2023-4]

FEP Protocol Builder

  • Ability to run FEP Protocol Builder on user defined submaps [2023-4]


  • Introduced the -parameter command line argument for to individually specify parameters [2023-4]
    • The -parameter argument expects a <key>=<value> argument, where <key> is one of several runtime parameters that can be inspected through the -write_param_file option.

Hit Identification & Virtual Screening

Ligand Preparation

Empirical and QM-based pKa Prediction

  • Improved Lewis structure canonicalization in Epik [2023-4]

Binding Site & Structure Analysis

Desmond Molecular Dynamics

  • Radial Distribution Function (RDF) Panel can now ‘Group’ sites by monomers [2023-4]

Mixed Solvent MD (MxMD)

  • Added support for fragment-size probes [2023-4]

Target Validation & Structure Enablement

AlphaFold Download / Process

  • Added support for processing AlphaFold2 models and PAE files created through ColabFold [2023-4]

Multiple Sequence Viewer/Editor

  • Full release of ‘Align by Family’ panel (removed beta label) [2023-4]
  • Added T-Cell receptors as newest protein family recognized and property annotated with sequence features [2023-4]
  • Support for family aware alignment of T-Cell Receptor sequences to enable downstream applications like homology modeling [2023-4]
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