Schrödinger Suites 2020-3
Schrödinger Suites 2020-3 | 13.9 Gb
Schrödinger, LLC. pleased to announce Schrödinger software release 2020-3. This quarterly release includes usability improvements and performance enhancements across all of our software.
Maestro Graphical Interface
- Rapidly and easily perform manual or guided lead optimization with the Ligand Designer [2020-3]
. “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)
Dock ligands from file
. 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). Add user properties from the PT.
. Send favorite designs for rank ordering by affinity with FEP+, for post-processing and dissemination in LiveDesign, or to Excel
- Faster rendering performance for the Looking Glass Holographic Display [2020-3]
- Resize the 2D Overlay [2020-3]
- Allow selection of residues at the protein-membrane interface [2020-3]
- 3D Builder: Build DNA and RNA Strands from Sequence [2020-3]
Multiple Sequence Viewer
Modernized design, new code, new capabilities
- Quick access to MSV from the main Window menu in Maestro or Tasks Menu. Improved user experience through an intuitive, easy to navigate interface that is similar in design to Maestro 11 [2020-3]
- Support for sequence alignment and comparison with options to set alignment method and adjust parameters [2020-3]
. Perform pairwise sequence alignment
. Perform multiple sequence alignment
. Generate a pairwise comparison matrix: compare entire sequences or selected columns based on similarity, identity or conservation
- Layer on and display information from various sources to enhance interpretation of differences or similarities between sequences [2020-3]
. Introduce global annotations
. Apply coloring by property
. View property metrics
. Rapidly and accurately annotate antibody CDR loops
. Rich set of in-buit sequence descriptors can be computed and values displayed in the metrics column next to the sequences.
. Flexibility to upload user-generated descriptors and color sequences by those properties.
- Homology Modeling: Guided step-by-step structure prediction workflows with checkmarks to indicate completed steps [2020-3]
. Find Homologs (BLAST)
. Many types of models are supported
Simple model: one target, one template
Chimeric model: one target, multiple templates
Batch models: multiple targets, one template
Multichain model: homo- and hetero-multimer
- Smooth integration with 3D structures in the Workspace [2020-3]
. Easily link and unlink sequence to structure
. Align structures based on entire sequence alignment or binding-site alignment
. One-click switching between split and combined chain representations
. Color sequence by structural property
. Apply sequence colors to workspace structure and vice versa
OPLS3e Force Field
- Schrodinger-ANI options to speed up fitting used by default and available via the FFB GUI [2020-3]
FEP+
- FEP+ Panel [2020-3]
. Integrated ForceField Builder + FEP Workflow
. Use QuickView to cycle through the edges’ mapping/hotregion data
. Ability to clear all/selected experimental data
. UX improvements to displaying Core SMARTS
. Eliminating redundant SMARTS patterns
. Highlight nodes that match core SMARTS
. GUI support to change # of lambda windows
- ABFEP Panel [2020-3]
. Support for multiple-ligand input
. Web services support
Molecular Dynamics
- Removal of Desmond CPU [2020-3]
Mixed Solvent MD (MxMD)
- Include probe structures that match each hotspot [2020-3]
Covalent Ligand Docking
- Apply user-defined constraints throughout refinement step [2020-3]
- Support for attachment atoms containing ‘ in the atom name ( ie nucleic acids) [2020-3]
Ligand Docking
- Apply Active Learning Glide to dock ultra-large libraries of billions of compounds using a combination of machine learning and Glide docking beta [2020-3]
Macrocycles
- Optionally provide inputs to macrocyclization script by input file [2020-3]
- Generate fusion protein peptide-linkers designs, ADC linkers, and fuse dimeric ligands with ability link disconnected molecules (command line only) [2020-3]
Induced Fit Docking
- IFD-MD Speed enhancements of approximately 5X without compromising accuracy [2020-3]
Pharmacophore Modeling
- Simplify application of create_hypoConsensus script which can now read the *.phypo format [2020-3]
Ligand Alignment
- Improve reference ligand specification by allowing to search for it [2020-3]
- Several bug fixes (e.g. tracebacks, job launch failures) [2020-3]
- Smaller default number of generated conformers for jobs based on flex_align to speed up calculation [2020-3]
- Adding tooltip [2020-3]
- Clarification on advanced option specification [2020-3]
Enumeration
- Improved reaction search by name by including description and name [2020-3]
Cheminformatics
- Create and apply Kohonen Self Organizing Maps from Canvas fingerprints or properties - beta [2020-3]
- Create and apply individual categorical and continuous QSAR models with full control over the features applied and machine learning - beta [2020-3]
. Create and make predictions with kPLS, MLR, PCR, Bayes or Recursive Partitioning machine learning techniques
. Employ a broad range of Canvas fingerprints, atomic and molecular descriptors, or user provided descriptors to create machine learning models
. Visualize atomic contributions from kPLS model predictions
. Automatic or manual creation of test/training set splits
Empirical and QM-based pKa Prediction
- Allow regular and customized OPLS3e force field for conformational search in Jaguar pKa [2020-3]
QM/MM (QSite)
- QSite now supports the OPLS3e force field [2020-3]
Quantum Mechanics
- Mössbauer spectroscopy [2020-3]
- Optionally use robust peaks when aligning VCD spectra with spectrum_align.py [2020-3]
- Compute thermochemical properties at a range of pressures [2020-3]
- Ring-chain tautomers can now be generated and scored in the AutoConf.py workflow [2020-3]
- .cosmo files for COSMO-RS calculations [2020-3]
- Batch calculations launched from the command line now optionally output and group failed subjobs to simplify their further processing [2020-3]
Binding Site Characterization
- Perform kinase binding site residue conservation analysis via new kinase_conservation_analysis.py script [2020-3]
- Returns pairs of residues that are unique enabling optimization of small molecules for selectivity
- Atom level properties annotate pairs of residues which are most unique across the gene family
Protein Homology Modeling
- Support for increased control of minimization parameters in all Prime refinement jobs ( loop predictions, sidechain predictions, binding site optimization etc) from the command-line [2020-3]
CryoEM
- Automated constraint weight scanning with PHENIX/OPLS3e to determine ideal weights [2020-3]
- PHENIX/OPLS3e - Stability improvements, multi coformer support, support for writing PDB files [2020-3]
Workflows & Pipelining
- Supports the latest version of KNIME (v4.2, but includes v4.1.3) [2020-3]
- Upload as LiveDesign model node [2020-3]
. Generic protocol taking any LiveReport column as input
. Pharmacophore hypotheses can be added to the LiveReport
. The models is created in the specified folder under Computational model
. The protocols and models can be uploaded via a python script
. Option to avoid KNIME version incompatibilities
- Any command line option can be used in the Glide ligand docking node [2020-3]
- Rapidly and easily perform manual or guided lead optimization with the Ligand Designer [2020-3]
. “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)
Dock ligands from file
. 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). Add user properties from the PT.
. Send favorite designs for rank ordering by affinity with FEP+, for post-processing and dissemination in LiveDesign, or to Excel
- Faster rendering performance for the Looking Glass Holographic Display [2020-3]
- Resize the 2D Overlay [2020-3]
- Allow selection of residues at the protein-membrane interface [2020-3]
- 3D Builder: Build DNA and RNA Strands from Sequence [2020-3]
Multiple Sequence Viewer
Modernized design, new code, new capabilities
- Quick access to MSV from the main Window menu in Maestro or Tasks Menu. Improved user experience through an intuitive, easy to navigate interface that is similar in design to Maestro 11 [2020-3]
- Support for sequence alignment and comparison with options to set alignment method and adjust parameters [2020-3]
. Perform pairwise sequence alignment
. Perform multiple sequence alignment
. Generate a pairwise comparison matrix: compare entire sequences or selected columns based on similarity, identity or conservation
- Layer on and display information from various sources to enhance interpretation of differences or similarities between sequences [2020-3]
. Introduce global annotations
. Apply coloring by property
. View property metrics
. Rapidly and accurately annotate antibody CDR loops
. Rich set of in-buit sequence descriptors can be computed and values displayed in the metrics column next to the sequences.
. Flexibility to upload user-generated descriptors and color sequences by those properties.
- Homology Modeling: Guided step-by-step structure prediction workflows with checkmarks to indicate completed steps [2020-3]
. Find Homologs (BLAST)
. Many types of models are supported
Simple model: one target, one template
Chimeric model: one target, multiple templates
Batch models: multiple targets, one template
Multichain model: homo- and hetero-multimer
- Smooth integration with 3D structures in the Workspace [2020-3]
. Easily link and unlink sequence to structure
. Align structures based on entire sequence alignment or binding-site alignment
. One-click switching between split and combined chain representations
. Color sequence by structural property
. Apply sequence colors to workspace structure and vice versa
OPLS3e Force Field
- Schrodinger-ANI options to speed up fitting used by default and available via the FFB GUI [2020-3]
FEP+
- FEP+ Panel [2020-3]
. Integrated ForceField Builder + FEP Workflow
. Use QuickView to cycle through the edges’ mapping/hotregion data
. Ability to clear all/selected experimental data
. UX improvements to displaying Core SMARTS
. Eliminating redundant SMARTS patterns
. Highlight nodes that match core SMARTS
. GUI support to change # of lambda windows
- ABFEP Panel [2020-3]
. Support for multiple-ligand input
. Web services support
Molecular Dynamics
- Removal of Desmond CPU [2020-3]
Mixed Solvent MD (MxMD)
- Include probe structures that match each hotspot [2020-3]
Covalent Ligand Docking
- Apply user-defined constraints throughout refinement step [2020-3]
- Support for attachment atoms containing ‘ in the atom name ( ie nucleic acids) [2020-3]
Ligand Docking
- Apply Active Learning Glide to dock ultra-large libraries of billions of compounds using a combination of machine learning and Glide docking beta [2020-3]
Macrocycles
- Optionally provide inputs to macrocyclization script by input file [2020-3]
- Generate fusion protein peptide-linkers designs, ADC linkers, and fuse dimeric ligands with ability link disconnected molecules (command line only) [2020-3]
Induced Fit Docking
- IFD-MD Speed enhancements of approximately 5X without compromising accuracy [2020-3]
Pharmacophore Modeling
- Simplify application of create_hypoConsensus script which can now read the *.phypo format [2020-3]
Ligand Alignment
- Improve reference ligand specification by allowing to search for it [2020-3]
- Several bug fixes (e.g. tracebacks, job launch failures) [2020-3]
- Smaller default number of generated conformers for jobs based on flex_align to speed up calculation [2020-3]
- Adding tooltip [2020-3]
- Clarification on advanced option specification [2020-3]
Enumeration
- Improved reaction search by name by including description and name [2020-3]
Cheminformatics
- Create and apply Kohonen Self Organizing Maps from Canvas fingerprints or properties - beta [2020-3]
- Create and apply individual categorical and continuous QSAR models with full control over the features applied and machine learning - beta [2020-3]
. Create and make predictions with kPLS, MLR, PCR, Bayes or Recursive Partitioning machine learning techniques
. Employ a broad range of Canvas fingerprints, atomic and molecular descriptors, or user provided descriptors to create machine learning models
. Visualize atomic contributions from kPLS model predictions
. Automatic or manual creation of test/training set splits
Empirical and QM-based pKa Prediction
- Allow regular and customized OPLS3e force field for conformational search in Jaguar pKa [2020-3]
QM/MM (QSite)
- QSite now supports the OPLS3e force field [2020-3]
Quantum Mechanics
- Mössbauer spectroscopy [2020-3]
- Optionally use robust peaks when aligning VCD spectra with spectrum_align.py [2020-3]
- Compute thermochemical properties at a range of pressures [2020-3]
- Ring-chain tautomers can now be generated and scored in the AutoConf.py workflow [2020-3]
- .cosmo files for COSMO-RS calculations [2020-3]
- Batch calculations launched from the command line now optionally output and group failed subjobs to simplify their further processing [2020-3]
Binding Site Characterization
- Perform kinase binding site residue conservation analysis via new kinase_conservation_analysis.py script [2020-3]
- Returns pairs of residues that are unique enabling optimization of small molecules for selectivity
- Atom level properties annotate pairs of residues which are most unique across the gene family
Protein Homology Modeling
- Support for increased control of minimization parameters in all Prime refinement jobs ( loop predictions, sidechain predictions, binding site optimization etc) from the command-line [2020-3]
CryoEM
- Automated constraint weight scanning with PHENIX/OPLS3e to determine ideal weights [2020-3]
- PHENIX/OPLS3e - Stability improvements, multi coformer support, support for writing PDB files [2020-3]
Workflows & Pipelining
- Supports the latest version of KNIME (v4.2, but includes v4.1.3) [2020-3]
- Upload as LiveDesign model node [2020-3]
. Generic protocol taking any LiveReport column as input
. Pharmacophore hypotheses can be added to the LiveReport
. The models is created in the specified folder under Computational model
. The protocols and models can be uploaded via a python script
. Option to avoid KNIME version incompatibilities
- Any command line option can be used in the Glide ligand docking node [2020-3]
Schrödinger Software provide accurate, reliable, and high performance computational technology to solve real-world problems in life science research. It can be used to build, edit, run and analyse molecules.
The Schrödinger-Suite of applications have a graphical user interface called Maestro. Using the Maestro you can prepare your structure for refinement.
The following products are available: CombiClide, ConfGen, Core Hopping, Desmond, Epik, Glide, Glide, Impact, Jaguar ( high-performance ab initio package), Liaison, LigPrep, MacroModel, MCPRO+, Phase, Prime, PrimeX, QikProp, QSite, Semi-Empirical, SiteMap, and Strike.
Jaguar: is an ab initio quantum chemistry software package developed by Schrodinger. It is rather fast, and has an extensive list of features. Some simple tasks (HF and DFT optimizations and closed-shell MP2 energies) can be performed in parallel. Jaguar can be used using a graphical user interface (see below) or by command line.
MacroModel: is a molecular modeling software package allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.
Schrödinger Release - New Features 2020-3
Schrödinger, LLC provides scientific software solutions and services for life sciences and materials research, as well as academic, government, and non-profit institutions around the world. It offers small-molecule drug discovery, biologics, materials science, and discovery informatics solutions; and PyMOL, a 3D molecular visualization solution. The company was founded in 1990 and is based in Portland, Oregon with operations in the United States, Europe, Japan, and India.
Product: Schrödinger Suites
Version: 2020-3
Supported Architectures: x64
Website Home Page : www.schrodinger.com
Language: english
System Requirements: PC / Linux *
Size: 13.9 Gb
Linux
Supported
- RedHat Enterprise Linux (RHEL) 6.10, 7.6-7.8, 8.1
For RHEL Server you must install some X11 libraries (sudo yum install fontconfig libX11).
- CentOS 6.10, 7.6-7.8, 8.1
For CentOS Server you must install some X11 libraries (sudo yum install fontconfig libX11).
For CentOS 8 you must install libnsl.
- Ubuntu 16.04 LTS, 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 SP1, 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 8.1 (requires contacting support for installation instructions)
- Windows 10, versions 1809, 1903, 1909, and 2004
We support English plus internationalized versions of the OS in Spanish, French, German, and Japanese.
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
Supported
- RedHat Enterprise Linux (RHEL) 6.10, 7.6-7.8, 8.1
For RHEL Server you must install some X11 libraries (sudo yum install fontconfig libX11).
- CentOS 6.10, 7.6-7.8, 8.1
For CentOS Server you must install some X11 libraries (sudo yum install fontconfig libX11).
For CentOS 8 you must install libnsl.
- Ubuntu 16.04 LTS, 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 SP1, 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 8.1 (requires contacting support for installation instructions)
- Windows 10, versions 1809, 1903, 1909, and 2004
We support English plus internationalized versions of the OS in Spanish, French, German, and Japanese.
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
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Added by 3% of the overall size of the archive of information for the restoration
No mirrors please
![Schrödinger Suites 2020-3]()
Added by 3% of the overall size of the archive of information for the restoration
No mirrors please
Schrödinger Suites 2020-3
