New Features
Software Releases
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]
ABFEP
- 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]
IFD-MD
- 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
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]
To view a list of known issues in Release 2023-2 please click here.