New Features

Format: Jun 2023
Format: Jun 2023

Hit Identification & Virtual Screening

Ligand Preparation and Conformation Generation

  • Full support for Epik 7 pKa predictions within the LigPrep interface and command line invocation [2023-2]

Empirical and QM-based pKa Prediction

  • Conjugate acid/base labels are now included in the Epik 7 log file [2023-2]

Hit Analysis

  • Release of the new Hit Analysis interface to streamline interactive analysis and selection of hits from virtual screening campaigns based on molecular properties, ligand feature locations, and shape alignments [2023-2]

Active Learning Applications

  • Added ability to train on preexisting FEP data for relative and absolute AL-FEP [2023-2]
  • Added histogram of compounds prioritized by machine learning for relative and absolute AL-FEP [2023-2]
  • Modified default machine learning settings to improve out-of-the-box performance of relative and absolute AL-FEP [2023-2]


  • New capability for fast filtering of inactive ligands to dramatically improve ABFEP throughput [2023-2]

Desmond Molecular Dynamics

  • Improved plotting for Trajectory Plots [2023-2]

Target Validation & Structure Enablement

Protein Preparation

  • Bond orders and charges can now either be re-assigned or only added to ligands and residues with missing bond orders [2023-2]

Protein X-Ray Refinement

  • Improved robustness when running Phenix/OPLS [2023-2]
  • New plots to inspect the best refinement statistics from Phenix/OPLS weight scans [2023-2]
  • Phenix/OPLS weight scan automatically choses a near-optimal combination of refinement parameters [2023-2]
  • Phenix/OPLS weight scan now returns MTZ files with map coefficients for each parameter combination [2023-2]

AlphaFold Download / Process

  • Downloaded AlphaFold structures are returned with an automatically created heatmap of the PAE matrix [2023-2]
  • Processed AlphaFold structures can now be optionally capped and the pLDDT threshold changed [2023-2]

Multiple Sequence Viewer/Editor

  • New ability for the detection and annotation of Vernier zone residues in antibodies [2023-2]


  • Added visual indicator when the target ligand is missing torsional parameters [2023-2]

Platform Environment

Maestro Graphical Interface

  • Added support for interactive nonstandard protein residue mutation via the Workspace context menu [2023-2]
  • Save up to 5K resolution GIFs (Workspace -> Animate) [2023-2]
  • Reduce unexpected visual clutter with new preference to limit the number of atom labels [2023-2]
  • Maestro to PyMOL connection [2023-2] 
    • Create a simple PyMOL movie from Maestro scenes 
  • Maestro to LiveDesign connection [2023-2]
    • Connect to LiveDesign servers with new access point and connection status indicator 
    • Retain and reuse single sign on (SSO) tokens to streamline the login process 
    • Benefit from a streamlined process of pushing Maestro data into LiveDesign via the Export panel 
  • Export Structures - New option to export MD-ready structure / trajectory to CMS file [2023-2]
  • New “Show Atom Properties (beta)” panel [2023-2]
    • List multiple atom properties for selected atoms
    • Display SMARTS/SMILES patterns for contiguous selected atoms, including the SMARTS index of the hovered-over atom

Workflows & Pipelining [KNIME Extensions]

  • Includes the latest version of KNIME [2023-2]
  • Improved usability of the Extract Properties node configuration panel [2023-2]
  • Updated LiveDesign nodes and protocols: [2023-2]
    • Adaptable input column checking of the LiveDesign input node
    • KNIME protocol section to install extra KNIME extensions is more robust

Lead Optimization


  • Improved atom mapping in FEP+ maps for macrocycles [2023-2]


  • New functionallity to auto-populate state populations in the FEP+ interface [2023-2]
  • Improved reporting of results in a single column (val ± err) in the overview tab of the FEP+ interface [2023-2]
  • Option to automatically merge force field parameters generated during an FEP+ job with those defined in your Maestro preferences [2023-2]
  • Option to select alternative water models for Relative Binding FEP+ via Advanced settings [2023-2]
  • Fast filtering of inactive ligands to dramatically improve ABFEP throughput [2023-2]
  • Improved atom mapping in FEP+ maps for macrocycles [2023-2]

Protein FEP

  • Ability to simultaneously predict protein thermostability with every protein/ligand selectivity simulation [2023-2]
  • Option to interactively edit perturbation topologies for protein residue mutations in FEP+ interface [2023-2]

Constant pH Simulations (Beta)

  • Greatly improved accuracy in protein pKa predictions through improved sampling of the physical end states of titratable residue side chains in FEP+ [2023-2]

Quantum Mechanics

  • New ability to plot excited state energies in rigid and relaxed coordinate scans [2023-2]
  • Support for alignment based on uniform scaling in the VCD/IR spectrum_align utility [2023-2]

Semi-Empirical Quantum Mechanics

  • Capability to use GFN2-xTB from within Jaguar and in Jaguar-based workflows [2023-2]
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