New Features

Format: Nov 2022
Format: Nov 2022
VIEW NEW FEATURES VIDEO

FEP+

  • Show user-friendly message when undefined stereochemical centers are introduced [2022-4]
  • Improved usability of FEP+ group panel to manage protonation and tautomeric states ensemble – for more accurate ΔΔG predictions [2022-4]

Constant pH Simulations (Beta)

  • Improved usability of constant pH simulations for protein pKa calculations with friendly outputs [2022-4}
     

Quantum Mechanics

  • Calculate ESP charges for excited states under the TDDFT/TDA approximation [2022-4]
  • Complete calculations faster with parallel Jaguar calculations on Windows [2022-4]
  • New Workflow Action Menu to guide to next steps for Plot Rigid/Relaxed scans [2022-4]
  • Over 80 examples of Jaguar input files in documentation [2022-4]

Target Validation & Structure Enablement

Protein Preparation

  • Significant speedup when opening the Protein Preparation Workflow interface on Windows [2022-4]
  • Reduced verbosity of Protein Preparation Workflow log file by limiting irrelevant CCD bond assignment error notices [2022-4]
  • Protein Reliability Report will generate TEST reflections on-the-fly, if not available in provided .cv file, and report RSCC values [2022-4]
  • Updated PROPKA to (latest) version 3.4 [2022-4]

Protein X-Ray Refinement

  • Introduction of GlideXtal command line tool for automatic ligand fitting in crystallographic electron density maps [2022-4]
  • PrimeX minimization is able to use structure factors in CIF format [2022-4]
  • In Phenix/OPLS can now remove all entities clashing with crystal mates [2022-4]
  • Phenix/OPLS is more robust to missing atoms in standard residues [2022-4]

Cryo-EM Model Refinement

  • Beta GlideEM interface for ligand placement into cryo-electron density maps [2022-4]
  • GlideEM now accepts gzipped (CCP4, MRC, MAP) files as input [2022-4]

Multiple Sequence Viewer/Editor

  • Beta release of Protein Family Alignment and Annotation [2022-4]
    • A new category named ‘Family Feature Calculation’ located in the ‘Other Tasks’
    • Menu exposes protein family alignment and annotation
    • Supports kinase and GPCR Alignments
    • Supports annotation of GPCR regions
  • Dendrogram hover tooltip to display distance information [2022-4]

IFD-MD

  • Membrane-bound IFD-MD tutorial [2022-4]
  • Covalent ligand IFD-MD tutorial [2022-4]

Solubility FEP (Beta)

  • Option to show solubility results in logS unit [2022-4]

Platform Environment

Maestro Graphical Interface

  • Create and share custom visualization Presets  [2022-4]
  • Added support to mutate DNA/RNA to standard nucleobases  [2022-4]
  • New Workflow Action Menu to guide to next steps for Plot Rigid/Relaxed scans [2022-4]
  • First full release of the new 2D sketcher [2022-4]
  • Get Going with Maestro Video Series added to Documentation [2022-4]

Workflows & Pipelining [KNIME Extensions]

  • Includes the latest version of KNIME (v4.6.1) [2022-4]
  • The number of matches can now be controlled in the Phase screening node [2022-4]

In LiveDesign:

  • When deploying a model the suitable KNIME protocol is chosen automatically and the latest version of the protocol uploaded [2022-4]
  • Distribution of calculations is controlled from the model admin page [2022-4]
  • Model changes from the LiveDesign Admin page can be preserved when overwriting an existing model [2022-4]
  • A new administration node to move, archive and unarchive models [2022-4]

Empirical and QM-based pKa Prediction

  • Initial release of Epik 7, a new machine learning based application for fast pKa value and protonation state prediction [2022-4]
    • Epik 7 can also produce a plot giving the populations of states as a function of pH

Desmond Molecular Dynamics

  • In Trajectory Plots view Ramachandran plot of Protein Residues [2022-4]

AutoQSAR

  • Added MACCs keys for ligand featurization in DeepAutoQSAR [2022-4]
  • Include ElasticNetCV model (strongly l1/l2 regularized linear regression) in DeepAutoQSAR hyper-parameter optimization [2022-4]
  • New DeepAutoQSAR command line utility for greater ease-of-use [2022-4]

Semi-Empirical Quantum Mechanics

  • GFN2-xTB method now available in the Semiempirical Module panel [2022-4]
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