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Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

  • Improved usability for several Project Table dialogs including Change Property, Substructure Count, Add Property, Add Sequential Index Property, Add Standard Molecular Property, Redo Calculation, and Total Surface Area
  • Improved usability of the Find Toolbar by adding a close button and “Search in Progress” indication

Workflows & Pipelining [KNIME Extensions]

  • Stabilized version of the KNIME generic LiveDesign protocols
  • New node for pKa prediction using Epik 7
  • Added support for AB-FEP files to FEP+ reader node

Target Validation & Structure Enablement

Protein Preparation

  • Improved accuracy of ligand ionization/tautomeric state predictions in the Protein Preparation Workflow using ML-enabled Epik by default
  • Ability to optionally provide sequence information via FASTA file when filling in missing loops

Multiple Sequence Viewer/Editor

  • Ability to export sequences and annotations to seqD file

Binding Site & Structure Analysis

Desmond Molecular Dynamics

  • Added Radial Distribution Function (RDF) analyzer in Trajectory Plots

Hit Identification & Virtual Screening

Ligand Preparation

Empirical and QM-based pKa Prediction

  • Improved accuracy in empirical corrections for Macro-pKa from a new ML-based algorithm used by default

Lead Optimization

FEP+

  • Improved functionality of FEP+ Panel-managed trajectories can now be moved out of the FEP+ entry group, to retain it in the project table

Protein FEP

  • Mutation generation will now ignore water molecules for sidechain placement

Solubility FEP

  • Ability to compute hydration free energies from Solubility FEP with useful blood brain barrier penetration correlation: Hydration-only mode is now available from Advanced Options of the Solubility FEP panel

Quantum Mechanics

  • Employ different basis sets by atom in Jaguar Transition Search
  • Predict and view NMR spectra based on DFT chemical shifts and spin-spin couplings
  • Added support for analytic basis sets with high angular momenta including cc-pvXz and def2 basis sets up to QZ
  • Added support for composite 3c-functionals: HF-3c, PBEh-3c, HSE-3c, B97-3c, r2SCAN-3c, and wB97X-3c

Biologics Drug Discovery

  • Improved accuracy in antibody modeling with new curated antibody database that now excludes redundant and/or poor-quality PDB structures
  • Option to export all 1000 unclustered raw poses from PIPER protein docking
  • Report the % humanness of the Heavy and Light chain on the grafted model in Antibody humanization by CDR grafting
  • Export aggregation profile images in png format
  • Report detailed patch characteristics in Protein Patch calculations
  • Easily perform detailed analysis of residue scanning results with new csv file containing mutant descriptions and energies

Materials Science

GUI for Quantum ESPRESSO

Product: Quantum ESPRESSO (QE) Interface

  • Convergence monitor for the nudged elastic band (NEB) calculations
  • Workflow for computing dielectric constant (command line)
  • Support for parallel computation of Phonon calculations (command line)
  • Option to display discrete frequencies from dynamical matrix for phonon DOS
  • Support for phonon calculations with Hubbard U potentials for LDA+U
  • Support for mean square displacement analysis over an existing AIMD trajectory

Materials Informatics

Product: MS Informatics

  • DeepAutoQSAR: Access from the Task menu under Materials Informatics
  • Formulation ML: Machine-learning-based property predictions using chemical formulations
  • Machine Learning Property: Improved machine learning models
  • MD Descriptors: Bond, angle, torsion, and vdW energies computed as descriptors
  • MD Descriptors: Improved efficiency with the MD simulation protocol

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG

  • CG FF Builder: Implicit charge assessment by dielectric constant
  • Automated DPD Mapping: Support for multiple ionization states (command line)
  • Automated DPD Mapping: Support for pre-defined patterns for use in mapping (command line)
  • Support for including CGFF file (*.json) information into other CGFF files

Reactivity

Product: MS Reactivity

  • Schrödinger Nanoreactor: Chemical reaction discovery and analysis module based on AIMD and semiempirical QM (xTB) methods
  • Auto Reaction Workflow: Improved speed in calculating custom rates and Keq

Microkinetics

Product: MS Microkinetics

  • Workflow module for microkinetic modeling of chemical reaction rates

MS Maestro Builders and Tools

  • Complex Enumeration: Support for the use of two ligand libraries as input
  • Complex Enumeration: Option to specify the number of unique ligands
  • Move Selected Atoms: Workspace tool to rotate/translate selected atoms

Classical Mechanics

  • Polymer Crosslink: Option to block formation of specific chemical structures
  • Molecular Deposition: UI update with improved control of adsorbate setup and simulation protocols

Quantum Mechanics

  • TST Rate: Jobs launched to queue

Education Content

  • New Tutorial: Microkinetic Modeling
  • New Tutorial: Machine Learning for Formulations
  • New Tutorial: Nanoreactor
  • New Tutorial: Modeling Receptor Binding in an Olfactory Protein
  • New Tutorial: Building a Coarse-Grained Skin Model using Martini Force Field
  • Updated Tutorial: Activation Energies for Reactivity in Solids and on Surfaces
  • Updated Tutorial: Molecular Deposition
Release 2023-4

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