New Features

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]

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]

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]

Ligand alignment

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

FEP+

• 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]

Macrocycles

• Introduced the -parameter command line argument for macrocyclize.py 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.

Ligand Preparation

Empirical and QM-based pKa Prediction

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