Schrodinger Suite 2024-3 Linux

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface
- Create customizable histograms from numerical data that are automatically synchronized with selection or filtering in other charts, the Project Table, or Workspace
- Improved support for T-Cell Receptors with display of their annotations in the Structure Hierarchy
Force Field
- Full release of the OPLS5 polarizable force field for organic atoms for improved FEP+ and Desmond model accuracy

Workflows & Pipelining (KNIME Extensions)

In LiveDesign:
- Ability to use a single generic protocol regardless of model input columns
- LiveDesign connection node can take credentials from the session rather than storing them in the workflow
- Date type columns are supported as LiveDesign model input

Binding Site & Structure Analysis

SiteMap
- Enable compact mode for sites with volume larger than a cutoff
- New RNA mode for improved performance of SiteScore for RNA
Desmond Molecular Dynamics
- New Unbinding Kinetics workflow to gain insights into drug-target residence time and optimize in vivo efficacy, safety profiles, and ADMET (beta)
- Analyze halogen bonds in SID Panel
- View local strain energy in “Torsion” tab of SID Panel
Mixed Solvent MD (MxMD)
- Improved organization of output structures and data in prjzip file

Hit Identification & Virtual Screening
- Streamline visualization of hits in the Hit Analyzer by outputting VSDB per docking run by default
- Streamlined generation of WScore models with new WScore Quick Model Generation panel (beta)

Ligand Preparation

Hit Analysis
- Filter chemotypes by SMARTS in Hit Analyzer Panel
FEP+
- Improved management of pKa/tautomer/conformer ensembles on ABFEP systems with Groups tab
- Core-SMARTS selection no longer requires selecting explicit hydrogen atoms
- Improved user interface allows more intuitive column sorting
- Export to LiveDesign now includes additional fields
- Edge analysis now includes halogen protein-ligand interactions
- Guided access to open FEP+ Panel for analysis upon calculation completion via Workflow Action Menus (WAM) in Maestro
Protein FEP
- New lambda dynamics (λD) enhanced protein residue mutation FEP+ for identifying high quality protein variants (beta)
- Expanded OPLS5 support for “Protein FEP” and “Protein FEP for Ligand Selectivity” panels
Solubility FEP
- Expanded OPLS5 support for Solubility FEP simulations
FEP Protocol Builder
- Gain up to 35% speedup in calculations due to changed defaults in the FEP Protocol Builder panel

Biologics Drug Discovery
- Perform DNA/RNA nucleobase mutations using residue scanning on command line via mut-pred.py
- Analyze DNA/RNA interactions with proteins in the Protein Interaction Analysis panel
- Search the non-standard residues library and find the closest matching natural amino acid analog
- Automatically annotate and number T Cell Receptor (TCR) structures using IMGT or AHo schemes
- Use pose-viewer files as input for Protein Interaction Analysis

Materials Science

GUI for Quantum ESPRESSO
Product: Quantum ESPRESSO (QE) Interface
- Check for the number of irreducible k-points from the panel
- Upgrade to Quantum ESPRESSO 7.3.1
- Quicker assessment of electric field for faster phonon calculations
- Force and stress information reported in the project table
- Option for more diagonalization algorithms for GIPAW steps (command line)
- Option to set separate driver and subjob hosts for NEB calculations
- Solid State NMR Viewer: Improved UI for selecting elements

Transport Calculations via MD simulations

Product: MS Transport
- Diffusion: Support for non-orthorhombic systems as input

Materials Informatics

Product: MS Informatics
- Formulation ML: Option to use Machine Learning Property predictions as descriptors
- Formulation ML: Option to use DeepAutoQSAR predictions as descriptors
- Machine Learning Property: Updates to existing models
- Machine Learning Property: Prediction of S1-T1 energy gap
- Machine Learning Property: Prediction of aqueous solubility
- Machine Learning Property: Output entries separated for each solvent

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG
- Coarse-Grained Force Field Builder: Automated mapping for dissipative particle dynamics (DPD)
- Coarse-Grained Force Field Builder: Visualization of CG mapping in the workspace

Reactivity

Product: MS Reactivity
- Nanoreactor: Frames from MD trajectory added to list of products
- Nanoreactor: Support for multistate (e.g. singlet-triplet) reactions
- Nanoreactor: Number of loaded structures reported in the viewer
- Nanoreactor: Plot for reactants (red) shown with products (blue) in the viewer
- Nanoreactor: Reactant structures to be included as standard output
- Reaction Workflow: Support for AutoTS output as input

Microkinetics

Product: MS Microkinetics
- Microkinetic Modeling: Support for renaming of reactions and participating species
- Microkinetic Modeling: Automatic population of molecular weight for gas/solute species
- Microkinetic Modeling: Automatic assigning of collision factor based on reaction type

MS Maestro Builders and Tools

- Solvate System: Option to neutralize systems with built-in counterions

Classical Mechanics

- Barrier Potential for MD: Support for NPT ensemble
- Elastic Constants: Option to reset the viewer panel
- Meta Workflows: Support for trajectory-based free volume analysis
- Order Parameter: Option to compute acentric order parameter
- Polymer Crosslink: Option to use a barrier potential
- Polymer Chain Analysis: Support for molecules with less than 40 atoms

Quantum Mechanics

- Adsorption Energy: Option to constrain atomic positions for systems with PBC
- Optoelectronic Film Properties: Workflow solution encompassing transition dipole moment orientation and singlet excitation energy transfer (SEET) calculations

Education Content

Life Science
- New Tutorial: Introduction to MD Trajectory Analysis with Desmond
- New Tutorial: Re-scoring Docked Ligands with MM-GBSA
- Updated Tutorial: Understanding and Visualizing Target Flexibility
- Updated Tutorial: Approximating Protein Flexibility without Molecular Dynamics
Materials Science
- New Tutorial: Singlet Excitation Energy Transfer
- New Tutorial: FEP Solubility
- New Tutorial: Genetic Optimization
- New Tutorial: Adsorption of Panthenol on Skin with All-Atom Molecular Dynamics
- Updated Tutorial: Applying Barrier Potentials for Molecular Dynamics Simulations
- Updated Tutorial: Automated Dissipative Particle Dynamics (DPD) Parameterization
- Updated Tutorial: Design of Asymmetric Catalysts with Automated Reaction Workflow
- Updated Tutorial: Machine Learning Property Prediction
- Updated Tutorial: Crosslinking Polymers