Library Background

Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

  • Dynamically display measurements based on selected atoms in the Status Bar
  • Copy fragments from existing molecules in the 3D Workspace and paste them onto selected atom(s) in another molecule
  • Export movies from the Trajectory Viewer with the Workspace resolution
  • Search in the Entry List using regular expressions for greater precision. Simultaneously search for multiple structures
  • Aligned pharmacophore label font with Maestro font preferences
  • Display T-cell receptor annotations in the Structure Hierarchy
  • Automatic synchronization of data point selection in scatter plots with Project Table selections and/or Workspace inclusion
  • Display data from different groups in a single scatter plot

Force Field

  • New OPLS5 Force Field (beta): Significant improvement in the accuracy of cation-pi and ionic group interactions via the addition of limited polarizability in relative binding-FEP+ and Desmond. Available as a new option alongside the default OPLS4

Workflows & Pipelining [KNIME Extensions]

  • Supports the latest version of KNIME (v5.2)
  • The Chemistry external tool node supports a new FEP+ column type that points to fmp files read by the FEP+ reader node

Binding Site & Structure Analysis


  • More accurate identification of RNA binding sites with 89% of RNA sites in HARIBOSS set now identified as the top-ranked binding site by SiteMap, up from 69% previously (beta)
  • New SiteMap parameters to separate large pockets that are bleeding into one another or across the protein surface and identify smaller distinct sites (command line only)

Mixed Solvent MD (MxMD)

  • Support for membrane systems

Hit Identification & Virtual Screening

Ligand Preparation

Active Learning Applications

  • Enhanced diversity selection in AL-Glide through consideration of up to 3x more compounds by horizontal scaling of diversity selection
  • Significantly improved LigandML prediction throughput in AL-Glide through use of ZMQ (command line only) (beta)
  • Much faster file uploading to the DriverNode in AL-Glide (command line only) (beta)

Ligand Docking

  • Improved pose-prediction and enrichment when docking small molecules into RNA receptors with Glide (beta)

Lead Optimization


  • Support setting up Positional Restraints in RB-FEP via FEP+ panel
  • Ability to use OPLS5 for Increased RB-FEP Accuracy
  • Improved Trajectory Management allowing trajectories from multiple edges in PT

Protein FEP

  • Support of Multi-Site Mutations for Thermostability prediction

Constant pH Simulations

  • Support of Lys pKa Calculations with panel support

Solubility FEP

  • Improved Trajectory Visualization
  • Link to Best Practices document
  • Support of Force Field Builder from Web Service

FEP Protocol Builder

  • Use FEP Protocol Builder to quickly identify FEP+ model parameters that optimize FEP+ accuracy using an automated machine learning-driven workflow
    • Free researcher time by letting the FEP Protocol Builder explore parameter space to identify and visualize optimal parameters for FEP+ model performance
    • Find FEP models for challenging systems through efficient exploration of parameter space
    • Proceed with confidence to use FEP+ prospectively in your program
    • Interface to set up FEP protocol optimization calculations with automated assignment of ligands into test/training sets
    • Interface to analyze influence of parameters on FEP model performance and compare protocol performance via FEP+ correlation plots

Quantum Mechanics

  • Perform wave function stability analysis in Jaguar
  • Generate NMR chemical shifts and spectra of 19F isotope with Jaguar Spectroscopy
  • Set multiplicity automatically (multip=2) if an odd number of electrons are found in Jaguar
  • Search for atropisomers using the new script (command line only)
  • More robust and performant E-sol workflow suitable for LiveDesign and command line execution 
  • Modify level of theory and basis sets of multiple entries with a right mouse click

Medical Chemistry Design

Ligand Designer

  • New Ring Swapping workflow to optimize lead compounds by exploring alternative ring scaffolds (beta)

Biologics Drug Discovery

  • Added 430 new non-natural amino acids to the library for use in peptide design
  • Interface improvements to speed analysis of protein mutation results produced by residue scanning
  • Analyze structural ensembles such as PIPER docking results and MD trajectories  with Protein-protein interaction analysis panel (open beta)
  • New option to specify one of five numbering schemes, Chothia, Kabat, IMGT, Enhanced Chothia or AHo, when performing antibody structure alignment using the script

Materials Science

GUI for Quantum ESPRESSO

Product: Quantum ESPRESSO (QE) Interface

  • Input for magnetization from structure data (command line)
  • Results viewer for solid state NMR spectra
  • NEB Convergence Monitor: Display of relative / activation energies
  • Automatic shift of K-point grids for improved convergence
  • Option to compute and visualize potential surfaces in the workspace
  • Phonon Density of States Viewer: Support for dielectric constant
  • Speed-up of NEB calculations with smart management of wave function data

KMC Charge Mobility

Product: MS Mobility

  • Compute KMC Charge Mobility: Charge transfer computed based on center-of-mass distances

Materials Informatics  

Product: MS Informatics

  • Formulation ML: Support for input data with missing component names / SMILES
  • Formulation ML: Support for Set2Set and graph-based models and descriptors added
  • Formulation ML: Option to remove highly-correlated descriptors (command line)
  • Formulation ML: Option to control the training set size
  • Formulation ML: Support for classification mode
  • Formulation ML: Feature-importance analysis based on Shapley additive explanations (SHAP)
  • Machine Learning Property: Improvements in prediction models available for download
  • Machine Learning Property: Prediction of oxidation and reduction potentials
  • MD Descriptors: Support for formulations-focused descriptors

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG

  • Coarse-Grained Force Field Builder: Automatically map atomistic systems to Martini particles (command line)
  • Coarse-Grained Force Field Builder: Fit Martini parameters (command line)


Product: MS Reactivity

  • Nanoreactor: Improved default settings
  • Nanoreactor: Speed-up of xTB frequency calculations
  • Nanoreactor: Improved deduplication algorithm for products
  • Nanoreactor: Improved parallelization algorithm
  • Nanoreactor: Option to remove high-energy products
  • Nanoreactor: xTB free energy used to rank-order products
  • Auto Reaction Workflow: Prevention of excessive equilibrium constant calculations from permutations


Product: MS Microkinetics

  • Microkinetic Modeling: Support for the use of analytical Jacobian
  • Microkinetic Modeling: Option to specify collision factor
  • Microkinetic Modeling: Results returned for cases that did not reach a steady state
  • Microkinetic Modeling: Option to list chemical equations from the input reaction network

Reactive Interface Simulator

Product: MS RIS

  • Solid Electrolyte Interphase: Reaction-template based solution for dynamic simulations of materials systems near battery electrodes

MS Maestro Builders and Tools

  • Density Profile: Visualization of density isosurfaces
  • Complex Builders: Option to clean up geometry using xTB
  • Semicrystalline Polymer: Support for polyvinyl alcohol (PVA)
  • Solvate System: Protocol to manage output with more than 2M atoms
  • Structured Liquid: Protocol to manage output with more than 2M atoms
  • Structured Liquid: Improved and expanded built-in lipid library

Classical Mechanics

  • Thermal Conductivity: Solution to predict thermal conductivity of solids

Quantum Mechanics

  • Adsorption Enumeration: Improved algorithm to define surface atoms
  • Adsorption Enumeration: Heavy-atom filter for reactive atoms
  • Amorphous NMR: Isosurface data available from QM calculations


Education Content

Life Science

  • New Tutorial: Ligand Binding Pose Prediction for FEP+ using Core-Constrained Docking (NEW)
  • New Tutorial: Ligand-Based Virtual Screening Using Phase (large-scale rework from the ground up)

Materials Science

  • New Tutorial: NMR Spectra Prediction
  • New Tutorial: Thermal Conductivity
  • New Tutorial: Solid Electrolyte Interphase Calculations
  • New Tutorial: Building a Semicrystalline Polymer
  • Updated Tutorial: Machine Learning for Formulations
  • Updated Tutorial: Update tutorials for switch to RDKit (affects multiple tutorials)
Release 2024-1

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