Schrodinger Suites 2021-3

Workflows & Pipelining [KNIME Extensions]

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

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]

Medicinal Chemistry Design

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]

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]