New Features
Software Releases
Software Releases
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]