New Features

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]

ABFEP

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

• Improved plotting for Trajectory Plots [2023-2]

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]

IFD-MD

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

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

Macrocycles

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

FEP+

• 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]