Schrodinger Suite 2024-2 Linux

Free Download Schrodinger Suite 2024-2 Linux | 10.7 Gb
The software developerSchrödingercontinuously strive to develop scientific solutions that push the boundaries of molecular design and are delighted to share enhanced drug discovery and materials workflows inSchrödinger’s 2024-2software release.
Owner:Schrödinger, LLC
Product Name:Schrödinger Suites
Version:2024-2 Commercial Version
Supported Architectures:x64
Website Home Page :www.schrodinger.com
Languages Supported:english
System Requirements:Linux *
Size:10.7 Gb

Schrödinger Software Release 2024-2 What’s new

Small Molecule Drug Discovery
Platform Environment
Maestro Graphical Interface
– Dynamically display measurements based on selected atoms in the Status Bar
– Copy fragments from existing molecules in the 3D Workspace and paste them onto selected atom(s) in another molecule
– Export movies from the Trajectory Viewer with the Workspace resolution
– Search in the Entry List using regular expressions for greater precision. Simultaneously search for multiple structures
– Aligned pharmacophore label font with Maestro font preferences
– Display T-cell receptor annotations in the Structure Hierarchy
– Automatic synchronization of data point selection in scatter Descriptions with Project Table selections and/or Workspace inclusion
– Display data from different groups in a single scatter Description
Force Field
– New OPLS5 Force Field: Significant improvement in the accuracy of cation-pi interactions and polarizable and ionic group interactions via the addition of limited polarizability via OPLS5 in relative binding-FEP+ and Desmond (beta)
Workflows & Pipelining [KNIME Extensions]
– Supports the latest version of KNIME (v5.2)
– The Chemistry external tool node supports a new FEP+ column type that points to fmp files read by the FEP+ reader node
Binding Site & Structure Analysis
SiteMap
– More accurate identification of RNA binding sites with 89% of RNA sites in HARIBOSS set now identified as the top-ranked binding site by SiteMap, up from 69% previously (beta)
– New SiteMap parameters to separate large pockets that are bleeding into one another or across the protein surface and identify smaller distinct sites (command line only)
Mixed Solvent MD (MxMD)
– Support for membrane systems
Hit Identification & Virtual Screening
Ligand Preparation
Active Learning Applications
– Enhanced diversity selection in AL-Glide through consideration of up to 3x more compounds by horizontal scaling of diversity selection
– Significantly improved LigandML prediction throughput in AL-Glide through use of ZMQ (command line only) (beta)
– Much faster file uploading to the DriverNode in AL-Glide (command line only) (beta)
Ligand Docking
– Improved pose-prediction and enrichment when docking small molecules into RNA receptors with Glide (beta)
Lead Optimization
FEP+
– Support setting up Positional Restraints in RB-FEP via FEP+ panel
– Ability to use OPLS5 for Increased RB-FEP Accuracy
– Improved Trajectory Management allowing trajectories from multiple edges in PT
Protein FEP
– Support of Multi-Site Mutations for Thermostability prediction
Constant pH Simulations
– Support of Lys pKa Calculations with panel support
Solubility FEP
– Improved Trajectory Visualization
– Link to Best Practices document
– Support of Force Field Builder from Web Service
FEP Protocol Builder
– Use FEP Protocol Builder to quickly identify FEP+ model parameters that optimize FEP+ accuracy using an automated machine learning-driven workflow
. Free researcher time by letting the FEP Protocol Builder explore parameter space to identify and visualize optimal parameters for FEP+ model performance
. Find FEP models for challenging systems through efficient exploration of parameter space
. Proceed with confidence to use FEP+ prospectively in your program
. Interface to set up FEP protocol optimization calculations with automated assignment of ligands into test/training sets
. Interface to analyze influence of parameters on FEP model performance and compare protocol performance via FEP+ correlation Descriptions
Quantum Mechanics
– Perform wave function stability analysis in Jaguar
– Generate NMR chemical shifts and spectra of 19F isotope with Jaguar Spectroscopy
– Set multiplicity automatically (multip=2) if an odd number of electrons are found in Jaguar
– Search for atropisomers using the new rotation_barriers.py script (command line only)
– More robust and performant E-sol workflow suitable for LiveDesign and command line execution
– Modify level of theory and basis sets of multiple entries with a right mouse click
Medical Chemistry Design
Ligand Designer
– New Ring Swapping workflow to optimize lead compounds by exploring alternative ring scaffolds (beta)
Biologics Drug Discovery
– Added 430 new non-natural amino acids to the library for use in peptide design
– Interface improvements to speed analysis of protein mutation results produced by residue scanning
– Analyze structural ensembles such as PIPER docking results and MD trajectories with Protein-protein interaction analysis panel (open beta)
– New option to specify one of five numbering schemes, Chothia, Kabat, IMGT, Enhanced Chothia or AHo, when performing antibody structure alignment using the align_antibody.py script
Materials Science
GUI for Quantum ESPRESSO
Product: Quantum ESPRESSO (QE) Interface
– Input for magnetization from structure data (command line)
– Results viewer for solid state NMR spectra
– NEB Convergence Monitor: Display of relative / activation energies
– Automatic shift of K-point grids for improved convergence
– Option to compute and visualize potential surfaces in the workspace
– Phonon Density of States Viewer: Support for dielectric constant
– Speed-up of NEB calculations with smart management of wave function data
KMC Charge Mobility
Product: MS Mobility
– Compute KMC Charge Mobility: Charge transfer computed based on center-of-mass distances
Materials Informatics
Product: MS Informatics
– Formulation ML: Support for input data with missing component names / SMILES
– Formulation ML: Support for Set2Set and graph-based models and descriptors added
– Formulation ML: Option to remove highly-correlated descriptors (command line)
– Formulation ML: Option to control the training set size
– Formulation ML: Support for classification mode
– Formulation ML: Feature-importance analysis based on Shapley additive explanations (SHAP)
– Machine Learning Property: Improvements in prediction models available for download
– Machine Learning Property: Prediction of oxidation and reduction potentials
– MD Descriptors: Support for formulations-focused descriptors
Coarse-Grained (CG) Molecular Dynamics
Product: MS CG
– Coarse-Grained Force Field Builder: Automatically map atomistic systems to Martini particles (command line)
– Coarse-Grained Force Field Builder: Fit Martini parameters (command line)
Reactivity
Product: MS Reactivity
– Nanoreactor: Improved default settings
– Nanoreactor: Speed-up of xTB frequency calculations
– Nanoreactor: Improved deduplication algorithm for products
– Nanoreactor: Improved parallelization algorithm
– Nanoreactor: Option to remove high-energy products
– Nanoreactor: xTB free energy used to rank-order products
– Auto Reaction Workflow: Prevention of excessive equilibrium constant calculations from permutations
Microkinetics
Product: MS Microkinetics
– Microkinetic Modeling: Support for the use of analytical Jacobian
– Microkinetic Modeling: Option to specify collision factor
– Microkinetic Modeling: Results returned for cases that did not reach a steady state
– Microkinetic Modeling: Option to list chemical equations from the input reaction network
Reactive Interface Simulator
Product: MS RIS
– Solid Electrolyte Interphase: Reaction-template based solution for dynamic simulations of materials systems near battery electrodes
MS Maestro Builders and Tools
– Density Profile: Visualization of density isosurfaces
– Complex Builders: Option to clean up geometry using xTB
– Semicrystalline Polymer: Support for polyvinyl alcohol (PVA)
– Solvate System: Protocol to manage output with more than 2M atoms
– Structured Liquid: Protocol to manage output with more than 2M atoms
– Structured Liquid: Improved and expanded built-in lipid library
Classical Mechanics
– Thermal Conductivity: Solution to predict thermal conductivity of solids
Quantum Mechanics
– Adsorption Enumeration: Improved algorithm to define surface atoms
– Adsorption Enumeration: Heavy-atom filter for reactive atoms
– Amorphous NMR: Isosurface data available from QM calculations
Education Content
Life Science
– New Tutorial: Ligand Binding Pose Prediction for FEP+ using Core-Constrained Docking (NEW)
– New Tutorial: Ligand-Based Virtual Screening Using Phase (large-scale rework from the ground up)
Materials Science
– New Tutorial: NMR Spectra Prediction
– New Tutorial: Thermal Conductivity
– New Tutorial: Solid Electrolyte Interphase Calculations
– New Tutorial: Building a Semicrystalline Polymer
– Updated Tutorial: Machine Learning for Formulations
– Updated Tutorial: Update tutorials for switch to RDKit (affects multiple tutorials)
Schrödinger Softwareprovide 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.
Schrödinger Release – New Features 2024-2
Schrödinger, LLCprovides 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.