New Features

Format: Jun 2023
Format: Jun 2023
VIEW NEW FEATURES VIDEO

Lead Optimization

Macrocycles

  • Improved atom mapping in FEP+ maps for macrocycles [2023-2]

FEP+

  • New functionallity to auto-populate state populations in the FEP+ interface [2023-2]
  • Improved reporting of results in a single column (val ± err) in the overview tab of the FEP+ interface [2023-2]
  • Option to automatically merge force field parameters generated during an FEP+ job with those defined in your Maestro preferences [2023-2]
  • Option to select alternative water models for Relative Binding FEP+ via Advanced settings [2023-2]
  • Fast filtering of inactive ligands to dramatically improve ABFEP throughput [2023-2]
  • Improved atom mapping in FEP+ maps for macrocycles [2023-2]

Protein FEP

  • Ability to simultaneously predict protein thermostability with every protein/ligand selectivity simulation [2023-2]
  • Option to interactively edit perturbation topologies for protein residue mutations in FEP+ interface [2023-2]

Constant pH Simulations (Beta)

  • Greatly improved accuracy in protein pKa predictions through improved sampling of the physical end states of titratable residue side chains in FEP+ [2023-2]

Quantum Mechanics

  • New ability to plot excited state energies in rigid and relaxed coordinate scans [2023-2]
  • Support for alignment based on uniform scaling in the VCD/IR spectrum_align utility [2023-2]

Semi-Empirical Quantum Mechanics

  • Capability to use GFN2-xTB from within Jaguar and in Jaguar-based workflows [2023-2]

FEP+

  • Significant performance improvements of up to 1.4X in FEP+ perturbations/day realized from collaboration with NVIDIA. The greatest speed boosts are observed on larger core count GPUs with small to moderate sized systems [2023-1]
  • Improved interface usability when handling groups, including how values are applied to maps [2023-1]
  • Automatically calculate protomer/tautomer/conformer populations using Epik7 with fep_groups.py script [2023-1]

Quantum Mechanics

  • Easily hide and redisplay spectra in the Spectrum Plot interface [2023-1]
  • Added support for rSCAN, r2SCAN, and r2SCAN-D3(BJ) DFT functionals [2023-1]
  • Added support for thirty-four D4 dispersion corrected functionals [2023-1]

Semi-Empirical Quantum Mechanics

  • Switch from MOPAC7.1 to MOPAC2016 calculation engine for Semiempirical interface [2023-1]

Hit Identification & Virtual Screening

Ligand Preparation and Conformation Generation

  • Full support for Epik 7 pKa predictions within the LigPrep interface and command line invocation [2023-2]

Empirical and QM-based pKa Prediction

  • Conjugate acid/base labels are now included in the Epik 7 log file [2023-2]

Hit Analysis

  • Release of the new Hit Analysis interface to streamline interactive analysis and selection of hits from virtual screening campaigns based on molecular properties, ligand feature locations, and shape alignments [2023-2]

Active Learning Applications

  • Added ability to train on preexisting FEP data for relative and absolute AL-FEP [2023-2]
  • Added histogram of compounds prioritized by machine learning for relative and absolute AL-FEP [2023-2]
  • Modified default machine learning settings to improve out-of-the-box performance of relative and absolute AL-FEP [2023-2]

ABFEP

  • New capability for fast filtering of inactive ligands to dramatically improve ABFEP throughput [2023-2]

Shape Screening

  • Easily restart Shape GPU calculations from the command line [2023-1]

Desmond Molecular Dynamics

  • Improved plotting for Trajectory Plots [2023-2]
  • Improvement in performance up to 1.17X (17%) in ns/day throughput realized from collaboration with NVIDIA. The largest speed improvements from running on modern GPUs with small to moderate sized systems [2023-1]
  • In Trajectory Plots view Ramachandran plot of Protein Residues [2022-4]

Target Validation & Structure Enablement

Protein Preparation

  • Bond orders and charges can now either be re-assigned or only added to ligands and residues with missing bond orders [2023-2]

Protein X-Ray Refinement

  • Improved robustness when running Phenix/OPLS [2023-2]
  • New plots to inspect the best refinement statistics from Phenix/OPLS weight scans [2023-2]
  • Phenix/OPLS weight scan automatically choses a near-optimal combination of refinement parameters [2023-2]
  • Phenix/OPLS weight scan now returns MTZ files with map coefficients for each parameter combination [2023-2]

AlphaFold Download / Process

  • Downloaded AlphaFold structures are returned with an automatically created heatmap of the PAE matrix [2023-2]
  • Processed AlphaFold structures can now be optionally capped and the pLDDT threshold changed [2023-2]

Multiple Sequence Viewer/Editor

  • New ability for the detection and annotation of Vernier zone residues in antibodies [2023-2]

IFD-MD

  • Added visual indicator when the target ligand is missing torsional parameters [2023-2]

Protein Preparation

  • Small peptides (< 200 atoms) can now also optionally be capped [2023-1]

Multiple Sequence Viewer/Editor

  • Use the Protein Family Alignment feature to align and annotate new sequences to a user supplied reference set for all protein families (beta) [2023-1]
  • Generate complement and reverse complement sequences for Nucleic Acid chains [2023-1]

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]

Platform Environment

Maestro Graphical Interface

  • Added support for interactive nonstandard protein residue mutation via the Workspace context menu [2023-2]
  • Save up to 5K resolution GIFs (Workspace -> Animate) [2023-2]
  • Reduce unexpected visual clutter with new preference to limit the number of atom labels [2023-2]
  • Maestro to PyMOL connection [2023-2] 
    • Create a simple PyMOL movie from Maestro scenes 
  • Maestro to LiveDesign connection [2023-2]
    • Connect to LiveDesign servers with new access point and connection status indicator 
    • Retain and reuse single sign on (SSO) tokens to streamline the login process 
    • Benefit from a streamlined process of pushing Maestro data into LiveDesign via the Export panel 
  • Export Structures - New option to export MD-ready structure / trajectory to CMS file [2023-2]
  • New “Show Atom Properties (beta)” panel [2023-2]
    • List multiple atom properties for selected atoms
    • Display SMARTS/SMILES patterns for contiguous selected atoms, including the SMARTS index of the hovered-over atom

Workflows & Pipelining [KNIME Extensions]

  • Includes the latest version of KNIME [2023-2]
  • Improved usability of the Extract Properties node configuration panel [2023-2]
  • Updated LiveDesign nodes and protocols: [2023-2]
    • Adaptable input column checking of the LiveDesign input node
    • KNIME protocol section to install extra KNIME extensions is more robust

Maestro Graphical Interface

  • Simultaneously mutate multiple selected nucleotides [2023-1]
  • Quickly select “Nucleic Acids” substructures in the Custom Sets editor dialogs [2023-1]
  • New Custom Presets functionality [2023-1]
    • Option to export subset of only selected presets
    • Expanded control with “Color by Element (Chain Name Carbons)” option
  • Improved “Maestro to PyMOL” capabilities [2023-1]
    • Improved discovery of “Send to PyMOL” option by moving it to the File menu
    • Option to include trajectory data in “Send to PyMOL” 
  • Preference to “Keep center of rotation fixed while translating” now enabled by default [2023-1]
  • Project Table / Entry List improvements [2023-1]
    • Automatically scroll to the original row of a Shortcut Row entry with a double-click  
    • Select rows where any of the included entries have atoms selected in the Workspace
  • Show/hide pharmacophore feature labels with the Annotations toggle [2023-1]
  • BioLuminate [2023-1]
    • Quickly select antibody-related segments such as CDRs, Fab, Fv and others with predefined selection sets
  • View, analyze and share molecular vibrations information with new Vibrations panel [2023-1]  
    • Easy-to-use playback controls and tight interaction with the Workspace
    • Save frames from vibration frequency animation as 3D structures 
    • Communicate with colleagues through exported movies of selected modes 

Workflows & Pipelining [KNIME Extensions]

  • Support for KNIME (v4.7) added [2023-1]
  • Enhanced robustness of the Extract Properties node where new properties can now be included or excluded [2023-1]
  • The LigPrep node now reads setting files exported from Maestro [2023-1]
  • The new Protein Preparation Workflow node configuration panel is identical to Maestro’s [2023-1]
  • Improvements to LiveDesign Import and Export nodes [2023-1]
    • Move beyond ligands and proteins to import any 2D/3D structure into LiveDesign as generic entities
    • Import entire LiveReports into KNIME for analysis

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]

AutoQSAR

AutoQSAR & DeepAutoQSAR

  • Normalize numeric additional features to eliminate instability in network training in case of very large or small values [2023-1]
  • 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]

QM/MM (QSite)

  • More robust and reliable minimizations from switching default minimizer from truncated newton to conjugate gradient [2023-1]
  • Added support for dispersion-corrected functionals including DFT-B3LYP-D3, DFT-M06-2X-D3, DFT-B3LYP-D3(BJ), DFT-M06-2X-D3(BJ), DFT-wB97X-D, and DFT-B97-D3 [2023-1]

Medicinal Chemistry Design

Ligand Designer

  • Design for ligand selectivity through visualization of binding site volumes accessible to only one of two receptors and identifying ligands that dock well into only one of two receptors (beta) [2023-1]

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]

Solubility FEP (Beta)

  • Option to show solubility results in logS unit [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

Semi-Empirical Quantum Mechanics

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