Schrödinger Suites 2021-2

Medicinal Chemistry Design

Ligand Designer
- Remember ‘Adjust view and style’ setting [2021-2]

Lead Optimization

Conformational Analysis

Ligand alignment
- Resolve issue when reference ligand changes inadvertently upon selection/inclusion changes [2021-2]
- Improvements for macrocycle alignment [2021-2]
. Improve presentation of macrocycle alignment results
. Check valid file path
. Harmonize which structure source options are available
- Improvement of custom atom weights table [2021-2]
Quantum Mechanics
- An automated mirror image of the VCD spectrum of a single enantiomer [2021-2]
- An improved solvent selector for implicit solvation models [2021-2]
- Fukui functions for radicals [2021-2]
- A more intuitive mechanism for specifying user-defined functionals in Jaguar input files [2021-2]
- Dynamic polarizabilities and hyperpolarizabilities are available in the Properties tab in Jaguar panels [2021-2]

Property Prediction

FEP+
- Automatic upgrade of outdated S-OPLS files [2021-2]
- Support for Linker enumeration for Covalent FEP [2021-2]
- Show edges protocol information [2021-2]
- Automated membrane-building within FEP+ Workflow [2021-2]
Protein FEP
- Multi-site mutation support in Protein FEP/Ligand Selectivity GUIs [2021-2]
- Protein Edge Analysis/PDF reports from the GUI [2021-2]
- Faster search filtering [2021-2]
- Improved handling of NSAA [2021-2]
- Correlation plots [2021-2]
Quantum Mechanics
- An automated mirror image of the VCD spectrum of a single enantiomer [2021-2]
- An improved solvent selector for implicit solvation models [2021-2]
- Fukui functions for radicals [2021-2]
- A more intuitive mechanism for specifying user-defined functionals in Jaguar input files [2021-2]
- Dynamic polarizabilities and hyperpolarizabilities are available in the Properties tab in Jaguar panels [2021-2]

Hit Identification & Virtual Screening

Hit Discovery

Shape Screening
- Quickly review ligand chemistry and overlap of key interactions with new pdf shape report showing the 2D structure of top-scoring hits and shape overlaps to probe features. [2021-2]
- Employ a Phase hypothesis as the shape query [2021-2]
Ligand Docking
- Add num_rescore_ligand option in Active Learning Glide time estimate panel [2021-2]
- Optionally provide your own grid file for Active Learning Glide experiment [2021-2]
- Support use of hydrogen bond and positional constraints in Active Learning Glide experiments from command line [2021-2]

Target Validation & Structure Enablement

Structure Enablement

Protein Preparation
- Improved donor-donor scoring function and water state enumeration in hydrogen bond network optimization of protassign [2021-2]
Protein X-Ray Refinement
- Speed loop refinement by avoiding recalculation of energies [2021-2]
Cryo-EM Model Refinement
- Support for constraints in Glide-EM (command-line only) [2021-2]
Multiple Sequence Viewer/Editor
- Added dendrogram advanced settings including choice of: tree layout, similarity matrix and tree type [2021-2]
- Created a color scheme for categorical residue properties [2021-2]
- Selecting and copying antibody CDR loops to New Tab in order to facilitate comparison of CDR's across multiple sequences [2021-2]
- Assigning job names when building homology models [2021-2]
- Display of 2D images of residue structure in tooltip - especially useful for visualizing structure of non-standard amino acids [2021-2]

Binding Site & Structure Analysis

Desmond Molecular Dynamics
- Visualize B factor and secondary structure in trajectory analysis RMSF plots [2021-2]

Platform Environment

Maestro Graphical Interface
- New “Import From Project” panel [2021-2]
. Improved data importing from other Maestro projects
- New rocking/rotating Workspace animation [2021-2]
. Save as animated GIF
- Improvements to “Export Structure” and “Save Project” dialogs (Windows only) [2021-2]
- Easily add zero-order bonds to molecules via the 2D sketcher [2021-2]
- Expanded R-group libraries to form targeted interactions [2021-2]
- Improved image rendering in the 2D Overlay [2021-2]
- New Workflow Action Menu for plotting Jaguar geometry optimization energies [2021-2]
Workflows & Pipelining [KNIME Extensions]
- Includes the latest version of KNIME (v4.3.2) [2021-2]
- New Ligand alignment node [2021-2]
- KNIME in LiveDesign [2021-2]:
. Generic protocols
More arguments fields to control the workflow
Control the computationally expensive calculation distribution
. Upload as LD model node
By default in the project that is set in the Preferences
A surface can be added to a receptor-ligand complex column
The models can also be uploaded from Maestro
. New LiveDesign connection node used as input for the Import and export to LiveDesign nodes

Linux

Supported
- RedHat Enterprise Linux (RHEL) 7.7-7.9, 8.1-8.3
For RHEL Server you must install some X11 libraries (sudo yum install fontconfig libX11).
- CentOS 7.7-7.9, 8.1-8.2
For CentOS Server you must install some X11 libraries (sudo yum install fontconfig libX11).
For CentOS 8 you must install libnsl.
- Ubuntu 18.04 LTS, and 20.04 LTS
For Ubuntu Server, user must also install some X11 libraries (sudo apt-get install fontconfig).
- SUSE: SLES/SLED 15 SP2, SLES/SLED 12 SP5

3D Support
- Supported: Quad-buffered OpenGL hardware stereo via NVIDIA 3D Vision, Interlaced stereo via Zalman 3D Monitors

Graphics Cards to Run Maestro
- Graphics card must support OpenGL 2.1 or greater
- We strongly recommend running Maestro using a discrete graphics card for optimal performance, though some integrated graphics cards show acceptable performance
Our software has been tested most robustly against multiple generations of NVidia graphics cards

Please note: Most graphics issues encountered are addressed by updating the graphics card driver. Please follow your hardware maker or OS distribution instructions to update the graphics driver

Windows

Please note:
- Only 64-bit platforms are supported.
- Processes that require a GPU are only supported on Linux.
- Jaguar cannot be run in parallel under Windows.

Supported
- Windows 10, versions 1909, 2004, and 20H2.
Please note: The multi-session version of Windows 10 Enterprise is not supported

3D Support
- Supported: Quad-buffered OpenGL hardware stereo via NVIDIA 3D Vision, Interlaced stereo via Zalman 3D Monitors

Graphics Cards to Run Maestro
- Graphics card must support OpenGL 2.1 or greater
- We strongly recommend running Maestro using a discrete graphics card for optimal performance, though some integrated graphics cards show acceptable performance
Our software has been tested most robustly against multiple generations of NVidia graphics cards

Please note: Most graphics issues encountered are addressed by updating the graphics card driver. Please follow your hardware maker or OS distribution instructions to update the graphics driver