New Features

Protein Preparation

• Reorganized and grouped Protein Prepwizard command line options for improved clarity and correspondence with the Maestro interface [2022-3]
• Improved valence error reporting in Diagnostics interface [2022-3]
• Several orders of magnitude speedup when assigning zero-order bonds and running the Epik stage in the Protein Prepwizard on large structures such as a ribosome [2022-3]
• Several times faster performance of ProtAssign when running on large structures with many small clusters or structures with a few large clusters [2022-3]
• Addition of -include_ligand_states flag in command line prepwizard and protassign scripts, to include Epik generated ligand states during the hydrogen bond assignment stage [2022-3]

Protein X-Ray Refinement

• Phenix/OPLS: Option to significantly improve computational performance by lowering the nonbonded energy term cutoff [2022-3]
  • A Phenix-side option schrodinger.flags.nonbonded_cutoff changes the cutoff. Default is to not change the cutoff. This has been tested with a cutoff of 10 angstrom, which increases computational efficiency by several times while no penalty to refinement statistics is observed.

Cryo-EM Model Refinement

• Introduced a new mode peptide for GlideEM, for enhanced peptide sampling with the command line parameter -nconformers specifying the number of conformers to generate [2022-3]
  • Additional input conformations are generated by running confgen on the peptide and redocking each conformation. The time and required computational resources required scale linearly with -nconformers
• Binding pocket / docking grid center can now be specified by binding site ASL and the ligand provided in a separate file in GlideEM [2022-3]
  • The binding site can be specified using the new -binding_site_asl command line argument, which requires an ASL that specifies residues near the binding site. The docking grid center will be the geometric mean of all atoms specified by the ASL. The ligand can be provided using the -ligand_struct command line argument

FEP+

• Drastically improved interactive performance of FEP+ Analysis tab interface with large maps with 100s of nodes edges [2022-3]
• Correlation plots will show pairwise ddG histogram (previously edgewise was shown) [2022-3]
• State Groupings GUI [2022-3]
  • Tautomers
  • Protomers
  • Conformers (binding poses)

Protein FEP

• Residue Mutation Selection layout change [2022-3]
  • Added support of CYM amino acid (deprotonated Cysteine)

Constant pH Simulations (Beta)

• The pH interval is fixed at 0.5 units and show number of resulting replicas [2022-3]

Solubility FEP

• Experimental ΔG data is shown in Analysis tab if the data is available [2022-3]

ABFEP

• Performance in ABFEP loading [2022-3]

Maestro Graphical Interface

• Apply styling and change molecular representations on selected entries [2022-3]
• New Workflow Action Menu support for Protein-Protein Docking [2022-3]
• “Send to PyMOL” panel preserves Maestro’s non-bonded interactions when viewed in PyMOL [2022-3]
• Create zero order bonds withing the 2D sketcher [2022-3]
• More reliable selection with improved accuracy of selecting atoms and bonds within the 2D sketcher [2022-3]
• Save user selection of authentication with LiveDesign by either credentials or single sign-on [2022-3]
• New Help icon provides access to relevant tutorials as well as documentation [2022-3]

Force Field

• Improvements to scalability of large FFBuilder jobs [2022-3]

Workflows & Pipelining [KNIME Extensions]

• Schrödinger extensions are compatible with KNIME 4.6 [2022-3]
• Create and apply ML models with new DeepAutoQSAR nodes [2022-3]