New Features

Ligand Preparation

Ligand Preparation and Conformation Generation

• Support CXSMILES enhanced stereochemistry information

Hit Discovery

Enumeration

• Support global and per-library concentrations when performing multiple R-group enumerations simultaneously [2021-3]

Pharmacophore Modeling

• Significant speedup of in-place pharmacophore screens against hypothesis with large numbers of features where few features are required to be matched. [2021-3]

Ligand Docking

• New input file format for Active Learning Glide simulations [2021-3]
• Allow separate specification of the number of simultaneous docking and ML prediction simulations to control license usage in Active Learning Glide [2021-3]
• Added counts of ligands that failed to dock for various reasons [2021-3]
• Return a CSV file of screened ligands by default [2021-3]
• Support Hydrogen bond and positional constraints in WScore [2021-3]

ABFEP

• Improved accuracy  by splitting complex leg lambda schedules for dihedral restraints from distance and angle restraints and ensuring overlap of cross-link restraints with the schedules of charge and vdW [2021-3] 

Structure Enablement

Protein Preparation

• First full release out of beta [2021-3]
• Renumber antibody residues using standard residue numbering for antibody naming scheme selected [2021-3]

Cryo-EM Model Refinement

• First full release out of beta for GlideEM and PHENIX/OPLS3e [2021-3]
• Support PHENIX 1.19.2 [2021-3]

Multiple Sequence Viewer/Editor

• Added kinase conservation annotation [2021-3]
• Homology modeling workflow improved to simplify template inclusion via file import or homolog searching [2021-3]

Binding Site & Structure Analysis

Desmond Molecular Dynamics

• Added support for Parrinello-Rahman barostat that allows for unit cell angle changes [2021-3]
• Added lipid-specific trajectory analysis [2021-3]

WaterMap

• Default forcefield for command line invocation changed to OPLS4 [2021-3]

Maestro Graphical Interface

• Recognize nucleic acid macromolecules as receptors [2021-3]
• Improved organization of multi-residue ligands (e.g. peptides) in the Structure Hierarchy [2021-3]
• New preference to “Allow nucleic acid molecules as ligands” [2021-3]
• New preference to “Avoid custom dialogs” (Windows 10 only) [2021-3]
• Label “Residue Information” on a selected atom [2021-3]
• New Protein Preparation Workflow as the default for Favorites toolbar and Prepare banner [2021-3]

Force Field 

• Improved accuracy of intracyclic torsion parameters for sulfonyl pyrroles [2021-3]

Workflows & Pipelining [KNIME Extensions]

• KNIME in LiveDesign:
  • Upload as LiveDesign model node [2021-3]
    • The extra argument and extra file fields are populated automatically 
    • The model folder can be set in the Preferences
  • Model administration [2021-3]
    • New node to list the deployed protocols and models 
    • Models can be archived using LiveDesign_admin.py

Ligand Designer

• Import custom R-groups for ideation directly from Ligand Designer [2021-3]
• Improve druglikeness of ideas generated by reaction-based enumeration by filtering out PAINS compounds and those that violate REOS or Schrodinger’s standard filters [2021-3] 

Conformational Analysis

Quantum Mechanics

• Added wB97X-D3 and wB97We X-V functional [2021-3]
• Improve control over the maximum number of simultaneous subjobs and parallelization with OpenMP threads [2021-3]
• Added ethanol, methanol, DMSO, and acetonitrile as solvents when predicting circular dichroism [2021-3]

Property Prediction

FEP+

• Simplify map visualization by clustering nodes with the same ligand in different charge/tautomer/conformation states [2021-3]

Protein FEP

• Examine correlations between experimental and FEP predicted affinities [2021-3]

Quantum Mechanics

• Enable alignment of theoretical and experimental IR spectra [2021-3]