New Features

FEP+

• Fit torsions on the fly via FFBuilder for FEP+ Web Services [2023-3] 
• Support linker enumeration of compounds with symmetrical R-groups [2023-3] 

Constant pH Simulations

• Full-featured release of constant pH simulations [2023-3]
• Improved analysis of constant pH simulations for protein pKa calculations [2023-3] 
  • Automatically write constant pH trajectories specific to each pH 
  • View trajectories from lambda dynamics calculations such as those from the constant pH workflow

Solubility FEP

• Fit torsions on the fly via FFBuilder for FEP+ Web Services [2023-3]

Quantum Mechanics

• Predict conformation-dependent IR and VCD/ECD spectra using an automated workflow within the new Jaguar Spectroscopy product [2023-3]
• Download importable Jaguar-formatted basis sets from Basis Set Exchange [2023-3] 
• Access dynamic scans from the Relaxed Scan panel [2023-3] 
• Access the ΔSCF method and a script to prepare ΔSCF input on the command line [2023-3] 

Semi-Empirical Quantum Mechanics

• Parallelize batch and individual xTB calculations with OpenMP [2023-3]

Ligand Preparation

Empirical and QM-based pKa Prediction

• Benefit from improved accuracy with the addition of several hundred more data points in the Macro-pKa training set [2023-3]

Active Learning Applications

• Adjust equilibration simulation times and complex restraint options in Active Learning-FEP [2023-3]
• Connect to ongoing GraphDB runs when restarting Active Learning-FEP jobs [2023-3]
• Generate a final Maestro file that contains all ligands with FEP data and the corresponding endpoints [2023-3]

Shape Screening

• Screen up to tens of billions of compounds quickly and efficiently with the new Quick Shape ligand-based screening workflow [2023-3]

ABFEP

• Fit torsions on the fly via FFBuilder for FEP+ Web Services [2023-3]

Protein Preparation

• Optionally use custom PFAM databases in pfam_driver.py [2023-3]
• Import structures into Coot with standard residue names from protein preparation’s PDB output. The Maestro output retains protonation-specific residue naming, i.e HIP/HID/HIE instead of HIS [2023-3]
• Significantly improved performance of Protein Preparation including the Interactive Optimizer for systems of 90,000 atoms or more [2023-3] 

Multiple Sequence Viewer/Editor

• Benefit from speed and accuracy improvements in protein/nucleic acid structure alignment from replacing the previous SKA aligner with the CEAlign algorithm [2023-3] 
• Download structural models directly from AlphaFold2 by providing a UniProt ID [2023-3]

IFD-MD

• Design out common ADMET liabilities using the new IFD-MD workflow (Beta). Predict complex structures of a ligand bound to CYP2D6, CYP3A4, PXR, or hERG [2023-3]

Maestro Graphical Interface

• Apply ribbon and cartoon styling on selected entries  [2023-3] 
• Improve visualization of interactions crossing Periodic Boundary Conditions [2023-3] 
• Seamlessly copy and paste data from the Project Table into external applications including spreadsheets, enabling efficient data transfer and analysis [2023-3] 
• Trajectory Player [2023-3] 
  • View trajectories from lambda dynamics calculations such as those from the constant pH workflow 
  • Navigate frames in trajectory visualization easily using keyboard arrow keys 
• 3D Builder [2023-3] 
  • Access Builder Behavior options from the 3D Builder palette
• Interactively mutate native nucleotides in the Workspace, including between DNA to RNA and RNA to DNA nucleotides [2023-3] 
• Enhanced "Save Project As" functionality with Windows-only UX improvements [2023-3] 
• Maestro to PyMOL connection [2023-3] 
  • Streamline the integration of WaterMaps with PyMOL
  • Include Maestro Scene "Description" as a PyMOL Message for better scene management
• Maestro to LiveDesign connection [2023-3] 
  • Seamlessly integrate between Maestro and LiveDesign with the new Mapping Manager. Easily rename property mappings and eliminate the issue of cluttered names when creating variations. Save and share mappings using the direct import and export feature.  

Job Control

• Smart distribution jobs in Job Server now check license availability, eliminating risk of license exhaustion [2023-3]

Workflows & Pipelining [KNIME Extensions]

• Streamline the login process with the LiveDesign connection node using Single Sign-On (SSO) tokens [2023-3]