New Features

Software Releases

Software Releases

Format: Sep 2020
Format: Sep 2020
VIEW NEW FEATURES VIDEO

Maestro Graphical Interface

  • Rapidly and easily perform manual or guided lead optimization with the Ligand Designer [2020-3]
    • “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)
      • Dock ligands from file
    • 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). Add user properties from the PT.
    • Send favorite designs for rank ordering by affinity with FEP+, for post-processing and dissemination in LiveDesign, or to Excel
  • Faster rendering performance for the Looking Glass Holographic Display [2020-3]
  • Resize the 2D Overlay [2020-3]
  • Allow selection of residues at the protein-membrane interface [2020-3]
  • 3D Builder: Build DNA and RNA Strands from Sequence [2020-3]
  • 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]
  • Allow selection of residues involved in interactions [2020-2]
  • Easily set measurements via the right-click context menu. [2020-2]

Multiple Sequence Viewer

Modernized design, new code, new capabilities

  • Quick access to MSV from the main Window menu in Maestro or Tasks Menu. Improved user experience through an intuitive, easy to navigate interface that is similar in design to Maestro 11 [2020-3]
  • Support for sequence alignment and comparison with options to set alignment method and adjust parameters [2020-3]
    • Perform pairwise sequence alignment
    • Perform multiple sequence alignment
    • Generate a pairwise comparison matrix: compare entire sequences or selected columns based on similarity, identity or conservation
  • Layer on and display information from various sources to enhance interpretation of differences or similarities between sequences [2020-3]
    • Introduce global annotations
    • Apply coloring by property
    • View property metrics
    • Rapidly and accurately annotate antibody CDR loops
    • Rich set of in-buit sequence descriptors can be computed and values displayed in the metrics column next to the sequences.
    • Flexibility to upload user-generated descriptors and color sequences by those properties.
  • Homology Modeling: Guided step-by-step structure prediction workflows with checkmarks to indicate completed steps [2020-3]
    • Find Homologs (BLAST)
    • Many types of models are supported
      • Simple model: one target, one template
      • Chimeric model: one target, multiple templates
      • Batch models: multiple targets, one template
      • Multichain model: homo- and hetero-multimer
  • Smooth integration with 3D structures in the Workspace [2020-3]
    • Easily link and unlink sequence to structure
    • Align structures based on entire sequence alignment or binding-site alignment
    • One-click switching between split and combined chain representations
    • Color sequence by structural property
    • Apply sequence colors to workspace structure and vice versa
  • 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]

OPLS3e Force Field

  • Schrodinger-ANI options to speed up fitting used by default and available via the FFB GUI [2020-3]
  • FFBuilder integration of the Schrodinger-ANI neural network for 2X faster fitting (command line only) [2020-2]

FEP+

  • FEP+ Panel [2020-3]
    • Integrated ForceField Builder + FEP Workflow
    • Use QuickView to cycle through the edges’ mapping/hotregion data
    • Ability to clear all/selected experimental data
    • UX improvements to displaying Core SMARTS
    • Eliminating redundant SMARTS patterns
    • Highlight nodes that match core SMARTS
    • GUI support to change # of lambda windows
  • ABFEP Panel [2020-3]
    • Support for multiple-ligand input
    • Web services support

Molecular Dynamics

  • Removal of Desmond CPU [2020-3]

Mixed Solvent MD (MxMD)

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

Covalent Ligand Docking

  • Apply user-defined constraints throughout refinement step [2020-3]
  • Support for attachment atoms containing ‘ in the atom name ( ie nucleic acids) [2020-3]

Ligand Docking

  • Apply Active Learning Glide to dock ultra-large libraries of billions of compounds using a combination of machine learning and Glide docking beta [2020-3]
  • 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]

Macrocycles

  • Optionally provide inputs to macrocyclization script by input file [2020-3]
  • Generate fusion protein peptide-linkers designs, ADC linkers, and fuse dimeric ligands with ability link disconnected molecules (command line only) [2020-3]
  • 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]

Induced Fit Docking

  • IFD-MD Speed enhancements of approximately 5X without compromising accuracy [2020-3]

Pharmacophore Modeling

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

Ligand Alignment

  • Improve reference ligand specification by allowing to search for it [2020-3]
  • Several bug fixes (e.g. tracebacks, job launch failures) [2020-3]
  • Smaller default number of generated conformers for jobs based on flex_align to speed up calculation [2020-3]
  • Adding tooltip [2020-3]
  • Clarification on advanced option specification [2020-3]
  • 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]

Enumeration

  • Improved reaction search by name by including description and name [2020-3]

Cheminformatics

  • 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

Empirical and QM-based pKa Prediction

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

QM/MM (QSite)

  • QSite now supports the OPLS3e force field [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]

Quantum Mechanics

  • Mössbauer spectroscopy [2020-3]
  • Optionally use robust peaks when aligning VCD spectra with spectrum_align.py [2020-3]
  • Compute thermochemical properties at a range of pressures [2020-3]
  • Ring-chain tautomers can now be generated and scored in the AutoConf.py workflow [2020-3]
  • .cosmo files for COSMO-RS calculations [2020-3]
  • Batch calculations launched from the command line now optionally output and group failed subjobs to simplify their further processing [2020-3]
  • 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]

Binding Site Characterization

  • Perform kinase binding site residue conservation analysis via new kinase_conservation_analysis.py script [2020-3]
    • Returns pairs of residues that are unique enabling optimization of small molecules for selectivity
    • Atom level properties annotate pairs of residues which are most unique across the gene family

Protein Homology Modeling

  • Support for increased control of minimization parameters in all Prime refinement jobs ( loop predictions, sidechain predictions, binding site optimization etc) from the command-line [2020-3]

CryoEM

  • Automated constraint weight scanning with PHENIX/OPLS3e to determine ideal weights [2020-3]
  • PHENIX/OPLS3e - Stability improvements, multi coformer support, support for writing PDB files [2020-3]

Workflows & Pipelining

  • Supports the latest version of KNIME (v4.2, but includes v4.1.3) [2020-3]
  • Upload as LiveDesign model node [2020-3]
    • Generic protocol taking any LiveReport column as input
    • Pharmacophore hypotheses can be added to the LiveReport
    • The models is created in the specified folder under Computational model
    • The protocols and models can be uploaded via a python script
    • Option to avoid KNIME version incompatibilities
  • Any command line option can be used in the Glide ligand docking node [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]

FPsim-GPU

  • Easily select or deselect all databases [2020-2]

Shape Screening

  • Split a GPU Shape bin file into multiple files for processing in parallel across multiple GPUs [2020-2]
To view a list of known issues in Release 2020-3 please click here.
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