Schrodinger Suites 2023.2

Platform Environment

Maestro Graphical Interface
- Added support for interactive nonstandard protein residue mutation via the Workspace context menu
- Save up to 5K resolution GIFs (Workspace -> Animate)
- Reduce unexpected visual clutter with new preference to limit the number of atom labels
- Maestro to PyMOL connection
. Create a simple PyMOL movie from Maestro scenes
- Maestro to LiveDesign connection
. 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
- New “Show Atom Properties (beta)” panel
. 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 (v4.7)
. (KNIME-6119)
- Improved usability of the Extract Properties node configuration panel
. (KNIME-6115, KNIME-6166, KNIME-6151, for Sanofi)
- Updated LiveDesign nodes and protocols:
. Adaptable input column checking of the LiveDesign input node
(KNIME-6156, for Interline. KNIME-6168, for Lilly)
. KNIME protocol section to install extra KNIME extensions is more robust
(KNIME-6136, KNIME-5608, for BP)

Lead Optimization

Macrocycles
- Improved atom mapping in FEP+ maps for macrocycles
FEP+
- New functionallity to auto-populate state populations in the FEP+ interface
- Improved reporting of results in a single column (val ± err) in the overview tab of the FEP+ interface
- Option to automatically merge force field parameters generated during an FEP+ job with those defined in your Maestro preferences
- Option to select alternative water models for Relative Binding FEP+ via Advanced settings
- Fast filtering of inactive ligands to dramatically improve ABFEP throughput
- Improved atom mapping in FEP+ maps for macrocycles
Protein FEP
- Ability to simultaneously predict protein thermostability with every protein/ligand selectivity simulation
- Option to interactively edit perturbation topologies for protein residue mutations in FEP+ interface
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+
Quantum Mechanics
- New ability to plot excited state energies in rigid and relaxed coordinate scans
- Support for alignment based on uniform scaling in the VCD/IR spectrum_align utility
Semi-Empirical Quantum Mechanics
- Capability to use GFN2-xTB from within Jaguar and in Jaguar-based workflows

Hit Identification & Virtual Screening

Ligand Preparation and Conformation Generation
- Full support for Epik 7 pKa predictions within the LigPrep interface and command line invocation
Empirical and QM-based pKa Prediction
- Conjugate acid/base labels are now included in the Epik 7 log file
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
Active Learning Applications
- Added ability to train on preexisting FEP data for relative and absolute AL-FEP
- Added histogram of compounds prioritized by machine learning for relative and absolute AL-FEP
- Modified default machine learning settings to improve out-of-the-box performance of relative and absolute AL-FEP
ABFEP
- New capability for fast filtering of inactive ligands to dramatically improve ABFEP throughput

Desmond Molecular Dynamics

- Improved plotting for Trajectory Plots

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
Protein X-Ray Refinement
- Improved robustness when running Phenix/OPLS
- New plots to inspect the best refinement statistics from Phenix/OPLS weight scans
- Phenix/OPLS weight scan automatically choses a near-optimal combination of refinement parameters
- Phenix/OPLS weight scan now returns MTZ files with map coefficients for each parameter combination
AlphaFold Download / Proces
- Downloaded AlphaFold structures are returned with an automatically created heatmap of the PAE matrix
- Processed AlphaFold structures can now be optionally capped and the pLDDT threshold changed
Multiple Sequence Viewer/Editor
- New ability for the detection and annotation of Vernier zone residues in antibodies
IFD-MD
- Added visual indicator when the target ligand is missing torsional parameters