Release Notes

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

LiveDesign

What’s upcoming in 2024-3

• Expansion of Biologics support in LiveDesign: Cognizant ingestion and representation of standard amino acid and nucleic acid based biologics, HELM support, customer-specific monomer database integration, in platform sequence analytics including initial SAR visualization mode, and 3D visualization improvements with ANARCI auto-annotated hierarchy
• New LiveDesign Learning module for rapid AI/ML molecular property predictions: Enables highly scalable, automated AI/ML pipelines for drug design
• Accelerated scaffold and R-group design with AutoDesigner Core Design: Automatically generate and optimize novel cores and R-group(s) simultaneously