New Features

Maestro Graphical Interface

• New “Import From Project” panel [2021-2]
  • Improved data importing from other Maestro projects 
• New rocking/rotating Workspace animation [2021-2]
  • Save as animated GIF
• Improvements to “Export Structure” and “Save Project” dialogs (Windows only) [2021-2] 
• Easily add zero-order bonds to molecules via the 2D sketcher [2021-2] 
• Expanded R-group libraries to form targeted interactions [2021-2] 
• Improved image rendering in the 2D Overlay [2021-2] 
• New Workflow Action Menu for plotting Jaguar geometry optimization energies [2021-2] 

Workflows & Pipelining [KNIME Extensions]

• Includes the latest version of KNIME (v4.3.2) [2021-2]
• New Ligand alignment node [2021-2]
• KNIME in LiveDesign  [2021-2]:
  • Generic protocols
    • More arguments fields to control the workflow
    • Control the computationally expensive calculation distribution
  • Upload as LD model node
    • By default in the project that is set in the Preferences
    • A surface can be added to a receptor-ligand complex column
    • The models can also be uploaded from Maestro
  • New LiveDesign connection node used as input for the Import and export to LiveDesign nodes

Ligand Designer

• Remember ‘Adjust view and style’ setting [2021-2]

Conformational Analysis

Ligand alignment

• Resolve issue when reference ligand changes inadvertently upon selection/inclusion changes [2021-2]
• Improvements for macrocycle alignment [2021-2]
  • Improve presentation of macrocycle alignment results
  • Check valid file path
  • Harmonize which structure source options are available
• Improvement of custom atom weights table [2021-2]

Quantum Mechanics

• An automated mirror image of the VCD spectrum of a single enantiomer [2021-2]
• An improved solvent selector for implicit solvation models [2021-2]
• Fukui functions for radicals [2021-2]
• A more intuitive mechanism for specifying user-defined functionals in Jaguar input files [2021-2]
• Dynamic polarizabilities and hyperpolarizabilities are available in the Properties tab in Jaguar panels [2021-2]

Property Prediction

FEP+

• Automatic upgrade of outdated S-OPLS files [2021-2]
• Support for Linker enumeration for Covalent FEP [2021-2]
• Show edges protocol information [2021-2]
• Automated membrane-building within FEP+ Workflow [2021-2]

Protein FEP

• Multi-site mutation support in Protein FEP/Ligand Selectivity GUIs [2021-2]
• Protein Edge Analysis/PDF reports from the GUI [2021-2]
• Faster search filtering [2021-2]
• Improved handling of NSAA [2021-2]
• Correlation plots [2021-2]

Quantum Mechanics

• An automated mirror image of the VCD spectrum of a single enantiomer [2021-2]
• An improved solvent selector for implicit solvation models [2021-2]
• Fukui functions for radicals [2021-2]
• A more intuitive mechanism for specifying user-defined functionals in Jaguar input files [2021-2]
• Dynamic polarizabilities and hyperpolarizabilities are available in the Properties tab in Jaguar panels [2021-2]

Hit Discovery

Shape Screening

• Quickly review ligand chemistry and overlap of key interactions with new pdf shape report showing the 2D structure of top-scoring hits and shape overlaps to probe features. [2021-2]
• Employ a Phase hypothesis as the shape query [2021-2]

Ligand Docking

• Add num_rescore_ligand option in Active Learning Glide time estimate panel [2021-2]
• Optionally provide your own grid file for Active Learning Glide experiment [2021-2]
• Support use of hydrogen bond and positional constraints in Active Learning Glide experiments from command line [2021-2]

Structure Enablement

Protein Preparation

• Improved donor-donor scoring function and water state enumeration in hydrogen bond network optimization of protassign [2021-2]

Protein X-Ray Refinement

• Speed loop refinement by avoiding recalculation of energies [2021-2]

Cryo-EM Model Refinement

• Support for constraints in Glide-EM (command-line only) [2021-2]

Multiple Sequence Viewer/Editor

• Added dendrogram advanced settings including choice of: tree layout, similarity matrix and tree type [2021-2]
• Created a color scheme for categorical residue properties [2021-2]
• Selecting and copying antibody CDR loops to New Tab in order to facilitate comparison of CDR's across multiple sequences [2021-2]
• Assigning job names when building homology models [2021-2]
• Display of 2D images of residue structure in tooltip - especially useful for visualizing structure of non-standard amino acids [2021-2]

Binding Site & Structure Analysis

Desmond Molecular Dynamics

• Visualize B factor and secondary structure in trajectory analysis RMSF plots [2021-2]

• Simplify application of create_hypoConsensus script which can now read the *.phypo format [2020-3]

• The 3D structure type (hence the rendering) and execution mode (automatic/run for each cell) can be controlled in the Upload model to LiveDesign node [2020-2]
• Surfaces and images can be added to the LiveReport [2020-2]
• New Prime Macrocycle Conformation sampling node [2020-2]
• The Molecule reader node takes in cif format [2020-2]
• The Export image to LiveDesign node supports SVG images [2020-2]

• New heteromultimer homology modeling workflow [2020-2]
• Associating data with sequences: Import per-residue data from experiment or predictions and visualize it mapped onto amino acid sequences [2020-2]

• Refined 3D building workflow [2020-4]
• In real-time identify similar purchasable compounds to design ideas. Requires FPsimGPU license sold separately. [2020-4]
• Expanded set of bioisosteres to include nitrogen walks [2020-4]
• Set clash colors for Growth Space [2020-4]
• Improved control of atom picking modes [2020-4]
• Validate and check ligands are congeneric before docking from file [2020-4]

• In MCS docking interface select to use flexible ligand alignment or produce docking-only alignments [2020-2]
• Dock from SMILES formats directly (*.smi or *.csv) with Glide to streamline virtual screening and facilitate large library screening [2020-2]

• Rapidly and easily perform manual or guided lead optimization with the Ligand Designer now in open beta [2020-2]
  • “Design your way” with automatic prediction of protein-ligand complex geometry
    • Whiteboard-like design in 2D
    • Design ligands in 3D without protein
    • Design ligands in 3D with simple view of protein interactions
    • Design in full 3D with protein
  • Overlay information critical to design
    • See regions of the binding pocket available for ligand growth
    • View protein-ligand interactions including clashes
    • View protein and ligand surfaces
    • View replaceable and displaceable water sites identified by WaterMap
    • Recognize ligand bonds amenable to common medicinal chemistry reactions
  • Guided workflows speed design
    • Bioisostere replacement
    • Isostere scanning
    • Replace or displace water sites
    • Form additional protein-ligand interactions
    • Cyclize ligands
    • Hybridize ligands (merge R-groups)
  • Tailor chemistry to your project with custom R-group libraries and property filters
  • Quickly assess molecular suitability with property-based radar plot (MW, logP, HBA, HBD, PSA)
  • Send favorite designs for rank-ordering by affinity with FEP+, for post-processing and dissemination in LiveDesign, or to Excel 
• Support for Looking Glass Holographic Display [2020-2]
  • https://lookingglassfactory.com/schrodinger
• Allow selection of residues involved in interactions [2020-2]
• Easily set measurements via the right-click context menu. [2020-2]

• Easily search, filter, and select from a large number of functionals and basis sets [2020-2]
• New functionals TPSS, SCAN, PKZB, SOGGA, SOGGA11, BOP [2020-2]
• Becke-Johnson’s and Sherrill’s dispersion corrections D3(BJ), D3M, and D3M(BJ) are available for a number of functionals [2020-2]
• Spectrum Plot panel can now visualize Jaguar-computed Raman spectra [2020-2]
• Script qm_descriptors.py which outputs QM descriptors now also outputs relative/absolute NMR shifts, Stockholder charges, and NBO charges [2020-2]
• Analytic NLO-V basis set optimized for polarizability calculations is available [2020-2]
• Maximum number of iterations in PBF implicit solvent calculations can be controlled by the keyword maxpbfit [2020-2]
• 1D/2D distributed_scan.py jobs output a .grd file even if some subjobs fail [2020-2]
• NMR chemical shifts are available for a number of dispersion-corrected functionals [2020-2]

• Improved alignments for congeneric series with common scaffolds defined by Bemis-Murcko scaffold or SMARTS [2020-2]
• Improve reference ligand specification [2020-2]
• Update or create new entries for aligned ligands [2020-2]

• Include probe structures that match each hotspot [2020-3]

• Create and apply Kohonen Self Organizing Maps from Canvas fingerprints or properties - beta [2020-3]
• Create and apply individual categorical and continuous QSAR models with full control over the features applied and machine learning - beta [2020-3]
  • Create and make predictions with kPLS, MLR, PCR, Bayes or Recursive Partitioning machine learning techniques
  • Employ a broad range of Canvas fingerprints, atomic and molecular descriptors, or user provided descriptors to create machine learning models
  • Visualize atomic contributions from kPLS model predictions
  • Automatic or manual creation of test/training set splits

• Split a GPU Shape bin file into multiple files for processing in parallel across multiple GPUs [2020-2]

• Allow regular and customized OPLS3e force field for conformational search in Jaguar pKa [2020-3]

• Dispersion-corrected functionals are now supported in the hydrogen-cap model [2020-2]
• The setting qsite_ff = opls3e in QSite input file activates OPLS3e [2020-2]

• Optionally provide inputs to macrocyclization script by input file [2020-2]
• Generate fusion protein peptide-linkers designs, ADC linkers, and fuse dimeric ligands with ability link disconnected molecules (command line only) [2020-2]

• FFBuilder integration of the Schrodinger-ANI neural network for 2X faster fitting (command line only) [2020-2]