New Features
Software Releases
Software Releases
Platform Environment
Maestro Graphical Interface
- Apply ribbon and cartoon styling on selected entries [2023-3]
- Improve visualization of interactions crossing Periodic Boundary Conditions [2023-3]
- Seamlessly copy and paste data from the Project Table into external applications including spreadsheets, enabling efficient data transfer and analysis [2023-3]
- Trajectory Player [2023-3]
- View trajectories from lambda dynamics calculations such as those from the constant pH workflow
- Navigate frames in trajectory visualization easily using keyboard arrow keys
- 3D Builder [2023-3]
- Access Builder Behavior options from the 3D Builder palette
- Interactively mutate native nucleotides in the Workspace, including between DNA to RNA and RNA to DNA nucleotides [2023-3]
- Enhanced "Save Project As" functionality with Windows-only UX improvements [2023-3]
- Maestro to PyMOL connection [2023-3]
- Streamline the integration of WaterMaps with PyMOL
- Include Maestro Scene "Description" as a PyMOL Message for better scene management
- Maestro to LiveDesign connection [2023-3]
- Seamlessly integrate between Maestro and LiveDesign with the new Mapping Manager. Easily rename property mappings and eliminate the issue of cluttered names when creating variations. Save and share mappings using the direct import and export feature.
Job Control
- Smart distribution jobs in Job Server now check license availability, eliminating risk of license exhaustion [2023-3]
Workflows & Pipelining [KNIME Extensions]
- Streamline the login process with the LiveDesign connection node using Single Sign-On (SSO) tokens [2023-3]
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]
Lead Optimization
FEP+
- Fit torsions on the fly via FFBuilder for FEP+ Web Services [2023-3]
- Support linker enumeration of compounds with symmetrical R-groups [2023-3]
Constant pH Simulations
- Full-featured release of constant pH simulations [2023-3]
- Improved analysis of constant pH simulations for protein pKa calculations [2023-3]
- Automatically write constant pH trajectories specific to each pH
- View trajectories from lambda dynamics calculations such as those from the constant pH workflow
Solubility FEP
- Fit torsions on the fly via FFBuilder for FEP+ Web Services [2023-3]
Quantum Mechanics
- Predict conformation-dependent IR and VCD/ECD spectra using an automated workflow within the new Jaguar Spectroscopy product [2023-3]
- Download importable Jaguar-formatted basis sets from Basis Set Exchange [2023-3]
- Access dynamic scans from the Relaxed Scan panel [2023-3]
- Access the ΔSCF method and a script to prepare ΔSCF input on the command line [2023-3]
Semi-Empirical Quantum Mechanics
- Parallelize batch and individual xTB calculations with OpenMP [2023-3]
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
Empirical and QM-based pKa Prediction
- Benefit from improved accuracy with the addition of several hundred more data points in the Macro-pKa training set [2023-3]
Active Learning Applications
- Adjust equilibration simulation times and complex restraint options in Active Learning-FEP [2023-3]
- Connect to ongoing GraphDB runs when restarting Active Learning-FEP jobs [2023-3]
- Generate a final Maestro file that contains all ligands with FEP data and the corresponding endpoints [2023-3]
Shape Screening
- Screen up to tens of billions of compounds quickly and efficiently with the new Quick Shape ligand-based screening workflow [2023-3]
ABFEP
- Fit torsions on the fly via FFBuilder for FEP+ Web Services [2023-3]
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]
Target Validation & Structure Enablement
Protein Preparation
- Optionally use custom PFAM databases in pfam_driver.py [2023-3]
- Import structures into Coot with standard residue names from protein preparation’s PDB output. The Maestro output retains protonation-specific residue naming, i.e HIP/HID/HIE instead of HIS [2023-3]
- Significantly improved performance of Protein Preparation including the Interactive Optimizer for systems of 90,000 atoms or more [2023-3]
Multiple Sequence Viewer/Editor
- Benefit from speed and accuracy improvements in protein/nucleic acid structure alignment from replacing the previous SKA aligner with the CEAlign algorithm [2023-3]
- Download structural models directly from AlphaFold2 by providing a UniProt ID [2023-3]
IFD-MD
- Design out common ADMET liabilities using the new IFD-MD workflow (Beta). Predict complex structures of a ligand bound to CYP2D6, CYP3A4, PXR, or hERG [2023-3]
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]
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]
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]
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]