Schrödinger Software Release 2020-2

Schrödinger Software Release Overview

Schrödinger announced their software release 2020-2, which is available for download now. This quarterly release includes usability improvements and performance enhancements across all of their software offerings.

What is Schrödinger used for?

Schrödinger develops state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research. Their physics based computational platform leverages a deep understanding of physics, chemistry, and predictive modeling to accelerate innovation in drug discovery. This allows collaborators to discover high-quality, novel molecules more rapidly, at lower cost, and most likely with a higher likelihood of success compared to traditional methods.

Changes since Release 2020-1

SMALL-MOLECULE DRUG DISCOVERY

Maestro Graphical Interface

• 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]
  • https://lookingglassfactory.com/schrodinger
• Allow selection of residues involved in interactions [2020-2]
• Easily set measurements via the right-click context menu. [2020-2]

Multiple Sequence Viewer

• 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

• FFBuilder integration of the Schrodinger-ANI neural network for 2X faster fitting (command line only) [2020-2]

FPsim-GPU

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

Ligand Docking

• 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 [2020-2]
• Generate fusion protein peptide-linkers designs, ADC linkers, and fuse dimeric ligands with ability link disconnected molecules (command line only) [2020-2]

Ligand Alignment

• 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]

Shape Screening

• Split a GPU Shape bin file into multiple files for processing in parallel across multiple GPUs [2020-2]

QM/MM (QSite)

• 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

• 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]

Workflows & Pipelining

• 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]

BIOLOGICS

General

• Added 2-aminobutryic acid (2AB) and 2-aminoisobutryic acid (Aib) to default non-native amino acid library [2020-2]
• In peptide docking select from recently used grids [2020-2]

MATERIALS SCIENCE

General

• GUI for Quantum ESPRESSO [2020-2]
  • Raman spectrum from periodic DFT (command-line)
  • Option to choose grid plane distance for convergence test
  • Support for use periodic DFT data in Elastic Constants Results
  • Access to D3 Grimme dispersion correction from GUI
  • DOS, PDOS, and charge density computed with hybrid functionals
• Transport Calculations via MD simulations [2020-2]
  • Driver for Diffusion Coefficient (CPU) to run separately from GPU MD
• Morphology Tools [2020-2]
  • Powder indexing removed from feature flag
    • External DICVOL installation as option (not requirement)
    • Prediction of Bravais lattice type
    • Support for exporting results

Builders and Tools

• Curve/Plot digitization tool [2020-2]
• Counterions with charged surfactants in Structured Liquid Builder [2020-2]
• Support for _atom_site_disorder_group in Crystal Builder [2020-2]
• Atom site labels in Crystal Builder [2020-2]
• Speed-up for building > 1M-atom system in Disordered System Builder [2020-2]
• Support for varying surface termination depth from Slabs and Interfaces [2020-2]

Classical Mechanics

• Averaging results from multiple sets of data for Stress Strain [2020-2]
• Yield strain prediction in Stress-Strain Analysis [2020-2]
• Uncertainty for yield strain marked in Stress-Strain Analysis [2020-2]
• Support for yield strain predictions in Uncertainty Quantification [2020-2]
• Improved error messages for failed residual strain calculations [2020-2]
• Support of stress-based prediction for Elastic Constants [2020-2]
• Option to selectively skip data in Uncertainty pooling analysis [2020-2]
• Tensors tab added in Elastic Constants Results [2020-2]
• All elastic/stress tensor components written to a log for Elastic Constants [2020-2]
• Option to generate PDF report from Thermophysical Properties Viewer [2020-2]
• MD Multistage relaxation protocols for semi-crystalline polymers [2020-2]
• Reduced use of disk space for H-bond autocorrelation calculation [2020-2]
• Option to run Polymer Chain Analysis on CPU for existing trajectories [2020-2]

Quantum Mechanics

• Reaction Workflow: Control of tolerance towards negative frequencies [2020-2]
• Reaction Workflow: Anharmonic corrections [2020-2]
• Improved rotation of η-ligands in Auto Reaction Workflow [2020-2]
• Restart option for Auto Reaction Workflow [2020-2]
• Support for substrate enumeration in Auto Reaction Workflow [2020-2]
• Improved Band Shape GUI logic with restart option [2020-2]
• Peak info written to *_bandshape_simplified.out for Band Shape [2020-2]
• Weakest bond energy reported for Bond and Ligand Dissociation Energy [2020-2]
• Computing energy gradient for double hybrid DFT functionals [2020-2]
• Option to create entries for all iterations from QM Convergence [2020-2]

Click here to view the new features video.

To view a list of known issues in Release 2020-2 please click here.