Release Notes

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

• Apple M1 Support [2022-1]
• New 2D Sketcher (beta) [2022-1]
• New Workflow Action Menus [2022-1]
  • Antibody Modeling
• Homology Modeling [2022-1]

Force Field

• Improved accuracy of histidine parameters, particularly in FEP+ prediction of histidine pka’s [2022-1]
• Improved geometries for B-N bond containing compounds [2022-1]
• Up to 10x faster execution of FFBuilder when parameterizing hundreds of ligands through greater job distribution [2022-1]

Workflows & Pipelining [KNIME Extensions]

• New 2D Sketcher node [2022-1]
• Run from LiveDesign [2022-1]:
  • Export to LiveDesign node can export all the structures so model results can be stored in new LiveReport(s)
  • Model output columns can contain files (eg with pdf)
  • Store an executed workflow in a LiveReport column

Target Validation & Structure Enablement

Protein Preparation

• Sped-up hydrogen atom assignment to be o(n) by system size [2022-1]

Protein X-Ray Refinement

• PHENIX/OPLS supports PHENIX 1.20 [2022-1]

Multiple Sequence Viewer/Editor

• Automatically save MSV projects [2022-1]
• Rapid selection of a subset of sequences based on user-defined percent identity or similarity relative to a reference sequence [2022-1]
• Improved ability to save one or more sequences by ‘right clicking’ to export [2022-1]

Protein Homology Modeling

• Selectively download only the PDB BLAST subset of the NR BLAST database for local homology modeling [2022-1]
• New Workflow Action Menu prompts for homology modeling enables single click access to structure quality assessment, reliability reports, additional loop refinement, and sidechain refinement and localized minimization [2022-1]

Hit Identification & Virtual Screening

Pharmacophore Modeling

• New align_multi_cores.py script to align 3D ligands to a reference ligand with multiple disconnected cores [2022-1]

Ligand Docking

• Return SMARTS of the core used when running core constraint docking with MCS [2022-1]
• Input file that generated a Glide grid is saved in the grid archive to improve ease of making changes [2022-1]

Lead Optimization

FEP+

• FEP+ Correlation Plot [2022-1]:
  • Display best fit line and equation of the line
  • Modified reporting to show confidence intervals instead of standard deviations
• Web services [2022-1]:
  • Improved performance when viewing map status

Solubility FEP (Beta)

• Access to trajectory, representative structures, FEP classifiers in the analysis tab [2022-1]
• Web Services will return fmp/fmpdb files instead of mae/csv for analysis [2022-1]

AutoQSAR

• DeepChemAutoQSAR now supports Windows and Mac platforms [2022-1]

FPsim-GPU

• New vendor column in similarity results [2022-1]

Medicinal Chemistry

Ligand Designer

• Ability to specify a max number of enumerated compounds [2022-1]
• Added access to “Vendor ID” details in the Project Table for purchasable compounds [2022-1]

Biologics Drug Discovery

• Antibody structure prediction backend now supports distributed processing facilitating large-scale, high-throughput workflows [2022-1]

Materials Science

GUI for Quantum ESPRESSO

• Atomic constraints propagated to phonon calculations [2022-1]
• Computing phonons for a subset of atoms [2022-1]
• IDPP (image dependent pair potential) algorithm for NEB [2022-1]
• Support for SCA and R2SCAN functionals [2022-1]

Materials Informatics

•  Molecular Descriptors: Speed-up of fingerprint calculations by parallelization [2022-1]
•  Molecular Descriptors: Organometallic descriptors for compounds with no metals [2022-1]

Coarse-Grained (CG) Molecular Dynamics

•  CG Forcefield Builder: GUI for automated force field building [2022-1]

Optoelectronics

•  Active Learning Optoelectronics: Plot for learning curves [2022-1]
•  Optoelectronics Genetic Algorithm: Option to use AutoQSAR and DeepChem models [2022-1]

Dielectric Properties

• Amorphous Dielectric Properties: Option to export data from the viewer [2022-1]

MS Maestro Builder and Tools

•  Crystal Builder: Option to select symmetry equivalent atoms [2022-1]
•  Manipulate Cell: Option to translate to first unit cell for 2 out of 3 axes [2022-1]
•  Manipulate Cell: Option to unwrap surface model within the periodic cell [2022-1]
• Structured Liquid Builder: Workflow action menu (WAM) [2022-1]

Classical Mechanics

• Cluster Analysis: Average cluster size and number of clusters in viewer [2022-1]
• Cluster Analysis: Option to visualize individual clusters [2022-1]
• Crystal Morphology: Estimation of the number of water molecules to solvate a slab (command-line) [2022-1]
• Membrane Analysis: Prediction of bilayer surface roughness [2022-1]
• Molecular Deposition: Default force constant at 500 kcal/mol/A [2022-1]
• Polymer Crosslinking: Speed-up (2x) by optimized simulation workflow [2022-1]
• Remove Molecules: Support for coarse-grained systems [2022-1]
• Stress Strain: User control of job hosts and license management [2022-1]
• Surface Tension: Workflow module to compute surface tension for a single-component system [2022-1]
• Thermochemical Properties: User control of job hosts and license management [2022-1]
• Thermochemical Properties: Option to choose energy recording interval [2022-1]
• Torsional Analysis: Option to plot relative torsion to initial state [2022-1]
• Torsional Analysis: Option to plot torsion distribution over time [2022-1]
• Torsional Analysis: Faster loading with reduced memory consumption [2022-1]
• Torsional Analysis: Support for coarse-grained structures [2022-1]
• Trajectory Density Analysis: No length limit on input ASL [2022-1]
• Trajectory Electrostatic Potential: Visualization module for radial charge profile and electrostatic potential in a trajectory [2022-1]

Quantum Mechanics

• Adsorption Energy: Thermochemical properties stored in CSV files [2022-1]
• Electron Coupling: Parallelization of QM calculations [2022-1]
• Excited State Analysis: Option to cluster by minimum of hole / electron correlation [2022-1]
• Excited State Analysis: Support for using multiple structures as input [2022-1]
• Ligand Stability Analysis: Stability assessment tool for organometallic complexes enumerated with different ligands [2022-1]
• Reaction Workflow: Buried volume data points stored as CSV file [2022-1]

Molecular Dynamics

Transport Calculations via MD simulations

• Diffusion: Visualization of 3D trajectory trace of a diffusing molecule [2022-1]
• Viscosity: Support for Einstein-Helfand viscosity [2022-1]
• Viscosity: Option to add diffusion calculation [2022-1]

LiveDesign

What’s new in LiveDesign 2022-1

• A new compound sketcher has been introduced, which was designed and developed by Schrodinger
• Add a compound to the sketcher by searching for its ID to use it as a basis for future designs
• Gadgets appear in a new location, along the left-hand panel, and can be grouped into categories to facilitate more rapid discovery of the appropriate gadget
• Computational modeling results can be aligned across columns on a per-pose basis, in order to identify related predicted values
• Tooltips can scroll to show long column descriptions when hovering over a column header

What’s been fixed

• MPOs with Freeform column inputs were not editable when copied from one project to another, and now are editable
• Unpublished clustering models showed duplicate values when a LiveReport was copied, and now show a single predicted value
• 3D data uploaded from Maestro would not appear in the Data & Columns tree, if the LiveDesign instance was configured to group experimental assays by concentration, and now will always appear
• Formula columns and Freeform columns could take several minutes to appear in a duplicated LiveReport, and now appear immediately
• The “Publish” button in the column menu of unpublished models would disappear after clicking it, and now will continue to appear
• Protocols that had a parameter set to optional could not have the parameter changed to mandatory, and now permit setting the parameter to mandatory
• LiveReport tabs could not be dragged and rearranged, and now can be dragged and rearranged
• Protocols that were made accessible in a project, and then made inaccessible to that project, would hide all models based on that protocol. The models now continue to appear in the Admin Panel
• Parameterized models would not display the column name in the Admin Panel when a Freeform column was used as the input parameter, and now display the column name
• Asynchronous tasks that took longer than the timeout period of eight days to complete were not canceled, and now are automatically canceled after eight days
• Creating models with optional parameters has an improved user interface