Schrodinger Suite 2023-4 Linux

Hit Identification & Virtual Screening

Ligand Preparation

Empirical and QM-based pKa Prediction
- Improved Lewis structure canonicalization in Epik [2023-4]

Binding Site & Structure Analysis

Desmond Molecular Dynamics
- Radial Distribution Function (RDF) Panel can now ‘Group’ sites by monomers [2023-4]
Mixed Solvent MD (MxMD)
- Added support for fragment-size probes [2023-4]

Target Validation & Structure Enablement

AlphaFold Download / Process
- Added support for processing AlphaFold2 models and PAE files created through ColabFold [2023-4]
Multiple Sequence Viewer/Editor
- Full release of ‘Align by Family’ panel (removed beta label) [2023-4]
- Added T-Cell receptors as newest protein family recognized and property annotated with sequence features [2023-4]
- Support for family aware alignment of T-Cell Receptor sequences to enable downstream applications like homology modeling [2023-4]

Platform Environment

Maestro Graphical Interface
- Improved functionality and enhanced usability in the new embedded Workspace Sequence Viewer [2023-4]
- Improved Scatter Plot capabilities: An updated charting tool provides a more intuitive interface, interactive features for data exploration, and extensive customization options for generating scatter plots [2023-4]
- New Lasso Selection: Draw a freeform selection path with superior precision around specific atoms or regions compared to Marquee Selection [2023-4]
- New 3D Builder behavior preference to automatically minimize newly added fragments [2023-4]
- Redesigned ‘Find Toolbar’ boasts an improved user interface with new functionalities such as sequence search and enhanced "Search by SMARTS" with access to the Sketcher [2023-4]
- Added support for Nonstandard Amino Acids in the 3D Builder [2023-4]
- Improved user interface for several Project Table dialogs [2023-4]:
. Combine Properties
. Copy Property
. Delete Properties
. Clear Values
- Added menu option to move selected entries to the top or end of their current group [2023-4]
- Enhanced surface visuals through texture mapping, utilizing per-vertex texture coordinates to enrich detail and color vibrancy [2023-4]
- mmCIF files (.cif) are now treated the same way as PDB files (.pdb) upon import into Maestro, with atoms automatically colored by element for improved visualization [2023-4]
Force Field
- FFBuilder now uses the QRNN-TB neural network potential as its default reference method. Typical FFBuilder jobs run 3-5X faster [2023-4]
Workflows & Pipelining [KNIME Extensions]
- LiveDesign connection node supports Single Sign-On and reconnection to hosts running different LiveDesign versions [2023-4]
. (KNIME-6251)
. (KNIME-6253)
- LiveDesign connection node can be connected to the Upload as LiveDesign node [2023-4]
. (KNIME-6255)
- LiveDesign settings are stored for several hosts as profiles in KNIME preferences panel [2023-4]
. (KNIME-6238, KNIME-5774)

Lead Optimization

Ligand alignment
- Improved performance of macrocycle alignment for cis- and trans-bond containing macrocycles [2023-4]
FEP+
- Improved analysis of multiple physical properties in FEP+ panel [2023-4]
. Small Molecule FEP: Relative Solvation, Relative Binding
. Solubility FEP: Hydration, Dissolution
. Protein FEP: Selectivity, Thermostability
- Additional settings in Advanced Options Panel [2023-4]
. Equilibration time
. Simulation time is split into solvent/complex/vacuum
- Improved accessibility for submitting jobs to web services [2023-4]
Constant pH Simulations
- Trajectory Player: Improvements to the Lambda Dynamics [2023-4]
FEP Protocol Builder
- Ability to run FEP Protocol Builder on user defined submaps [2023-4]
Macrocycles
- Introduced the -parameter command line argument for macrocyclize.py to individually specify parameters [2023-4]
. The -parameter argument expects a <key>=<value> argument, where <key> is one of several runtime parameters that can be inspected through the -write_param_file option.