Schrödinger Suites 2017-2

Schrödinger, LLC. pleased to announce Schrödinger software release 2017-2. This quarterly release includes usability improvements and performance enhancements across all of our software.

What's new in Schrödinger software release 2017-2:

Maestro Graphical Interface
- Improved R-group enumeration capabilities [ 2017-2 ]
. Easily create and manage custom R-group libraries
. Add R-group fragments to custom libraries from sketcher or by SMARTS matching against a set of compounds
- Up to 10x faster job incorporation for large number of structures [ 2017-2 ]
- Improved accuracy of “Drag and Drop” in the Project Table [ 2017-2 ]
- Entry List text searches now include group names [ 2017-2 ]
- Optionally expand all groups in the Project Table with selected entries [ 2017-2 ]
- Move “Stars” column anywhere in the Project Table [ 2017-2 ]
- Optionally cancel quick minimization (Ctrl-M) [ 2017-2 ]
- Restored Ctrl-G shortcut for Move Atoms mode [2017-2 ]
- Optionally include Workspace Properties in saved images [ 2017-2 ]
- Improved accessibility of apply measurements to conformers via right click menu [ 2017-2 ]
- Added ability to place fragments in Workspace not attached to an existing compound [ 2017-2 ]
- Increased functionality accessible from the Property Tree menu
- Better support for high resolution displays [ 2017-2 ]
- Schrodinger Academy tutorials from training seminars covering a wide range of topics now available in documentation [ 2017-2 ]


FEP+
- Reimagined panel to perform FEP+ perturbations of protein-ligand complexes (Beta) [ 2017-2 ]
. At-a-glance view of structural and binding affinity data to assess prediction quality and guide decision making
. Improve how the ligands are added to the already existing FEP Map. Ligands can now be added directly from either 2d Sketcher, file, or project table
. A new ‘Activity Cliff’ view of FEP+ results allows for easy recognition of compounds that are predicted to be potent or matched pairs with large free energy changes with small structural variation
. Improved Hysteresis Analysis
. Powerful interactive plotting, tying data to structures
Structure activity relationship (SAR) plot now with additional statistics describing experimental agreement
Activity cliffs
FEP SID analysis
. Export data to Excel, CSV or images that can be imported into PowerPoint
- Perform protein mutations with FEP to explore the the implication of a mutation(s) in the context of protein stability or its affinity with another protein (PPI) [ 2017-2 ]
- Perform Free Energy Perturbations of Macrocycles with FEP+ (Beta) [ 2017-2 ]
. Cyclize linear molecules into macrocycles
. Evaluate effect of changing macrocycle ring size
. Predict affinity differences for macrocycle sidechain variation
- FEP+ for Small Molecules [ 2017-2 ]
. Improved atom mapping for terminal rings


Molecular Dynamics
- Calculate molecule-to-molecule radial distribution functions with new ability to use center of charge, centroids, or center of mass [ 2017-2 ]
- New command line scripts for trajectory processing [ 2017-2 ]
. center.py – centers selection to the origin
. cluster.py – cluster trajectories based on RMSD of a selection
. occupancy.py – generates 3d occupancy grid based on a selection
. parch.py – reduce the size of a trajectory by removing unneeded water molecules
. rdf.py – calculates radial distribution function
. superimpose.py – align trajectory on a selection of atoms
. trj2mae.py – convert trajectory frames to maestro files
Ligand Docking
- Improved accuracy in docking macrocycles with Glide [ 2017-2 ]
- Glide now supports docking ligands with silicon atoms [ 2017-2 ]
- glide_sort now supports reverse sorting of large files [ 2017-2 ]
- Provide grids or receptor structures as input to XGlide [ 2017-2 ]
Macrocycles
- Optionally preserve major ring shape in Macrocycle Sampling [ 2017-2 ]
- Improved accuracy in docking macrocycles with Glide [ 2017-2 ]
- Perform Free Energy Perturbations of Macrocycles with FEP+ [ 2017-2 ]
Protein-Ligand Database (PLDB)
- Maestro GUI [ 2017-2 ]
. Assign residue types faster by mousing over residue blobs and entering three-letter code in the sketcher


AutoQSAR
- Easily convert affinity data to log scale with all predictions returned in the input units (backend only) [ 2017-2 ]
Empirical and QM-based pKa Prediction
- Review and adjust conformations treating them with Jaguar pKa [ 2017-2 ]
Workflows & Pipelining
- New AutoQSAR node [ 2017-2 ]
- KNIME_batch.py takes .knwf workflow extensions [ 2017-2 ]
- Confgen node uses Confgenx fast 3D Conformation generator [ 2017-2 ]
OPLS3 Force Field
- OPLS3 with virtual sites now default for minimizations run by Python minimize class (minimize.py) [ 2017-2 ]
- Improved FFBuilder efficiency [ 2017-2 ]
- Reduced propensity of chemical reaction failures [ 2017-2 ]
Ligand Preparation and Conformation Generation
- Optimized ligand minimization algorithm for speed [ 2017-2 ]
. Generate minimized conformers 30% faster with ConfGen
. Prepare ligands 10% faster with LigPrep
Pharmacophore Modeling
- Greater control over ligand grouping in common pharmacophore perception [ 2017-2 ]
. Group automatically by stereoisomers, title, or create groups manually
- Optionally employ custom features when creating hypotheses from protein-ligand complexes with epharmacophores workflow [ 2017-2 ]
- Improved tracking of progress in ligand screening [ 2017-2 ]
- Improved performance of sorting in screening jobs [ 2017-2 ]
Cheminformatics
- Distribute generation of property and topological descriptors across multiple CPUs [ 2017-2 ]


Quantum Mechanics
- Power user input of keywords for all Jaguar panels [ 2017-2 ]
- Print frequency contributions to thermal properties [ 2017-2 ]
- Customizable workflow to generate tautomers and conformers and rank them by the energy [ 2017-2 ]
. Command-line only
Semi-Empirical Quantum Mechanics
- Semi-empirical NDDO and MOPAC2012 batch jobs can run simultaneously on multiple CPU’s (distributed parallelization) [ 2017-2 ]
Protein Preparation
- Added support for complexes with iodine atoms [ 2017-2 ]
- Loosened threshold for RSCC flagging in protein reliability report to 0.8 [ 2017-2 ]
Protein X-Ray Refinement
- Added support for all standard space groups in RCSB PDB structures [ 2017-2 ]




About Schrödinger software Schrodinger 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.

About Schrödinger, LLC 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: 2017-2
Supported Architectures: 32bit / 64bit
Website Home Page : www.schrodinger.com
Language: english
System Requirements: PC / MacOsx / Linux
Supported Operating Systems: Windows 7even or newer / macOS 10.12 or Mac OS X 10.10 - 10.11 / RedHat Enterprise Linux (RHEL) 6.7-6.9, 7.2-7.3, CentOS 6.7-6.9, 7.2-7.3, Ubuntu 14.04 LTS, and 16.04 LTS, SUSE: SLES 12 SP2, SLED 12 SP2
Size: 17.1 Gb