[行业软件]Schrodinger Suite 2024-1 Advanced Edition [复制链接]

The software developer Schrödinger continuously strive to develop scientific solutions that push the boundaries of molecular design and are delighted to share enhanced drug discovery and materials workflows in Schrödinger’s 2024-1 software release.

Schrödinger Software Release 2024-1 What's new



New features


Small Molecule Drug Discovery

Platform Environment
Maestro Graphical Interface
- Improved usability for several Project Table dialogs including Change Property, Substructure Count, Add Property, Add Sequential Index Property, Add Standard Molecular Property, Redo Calculation, and Total Surface Area
- Improved usability of the Find Toolbar by adding a close button and “Search in Progress” indication
Workflows & Pipelining [KNIME Extensions]
- Stabilized version of the KNIME generic LiveDesign protocols
- New node for pKa prediction using Epik 7
- Added support for AB-FEP files to FEP+ reader node
Target Validation & Structure Enablement
Protein Preparation
- Improved accuracy of ligand ionization/tautomeric state predictions in the Protein Preparation Workflow using ML-enabled Epik by default
- Ability to optionally provide sequence information via FASTA file when filling in missing loops
Multiple Sequence Viewer/Editor
- Ability to export sequences and annotations to seqD file
Binding Site & Structure Analysis
Desmond Molecular Dynamics
- Added Radial Distribution Function (RDF) analyzer in Trajectory Plots

Hit Identification & Virtual Screening

Ligand Preparation
Empirical and QM-based pKa Prediction
- Improved accuracy in empirical corrections for Macro-pKa from a new ML-based algorithm used by default
Lead Optimization
FEP+
- Improved functionality of FEP+ Panel-managed trajectories can now be moved out of the FEP+ entry group, to retain it in the project table
Protein FEP
- Mutation generation will now ignore water molecules for sidechain placement
Solubility FEP
- Ability to compute hydration free energies from Solubility FEP with useful blood brain barrier penetration correlation: Hydration-only mode is now available from Advanced Options of the Solubility FEP panel
Quantum Mechanics
- Employ different basis sets by atom in Jaguar Transition Search
- Predict and view NMR spectra based on DFT chemical shifts and spin-spin couplings
- Added support for analytic basis sets with high angular momenta including cc-pvXz and def2 basis sets up to QZ
- Added support for composite 3c-functionals: HF-3c, PBEh-3c, HSE-3c, B97-3c, r2SCAN-3c, and wB97X-3c

Biologics Drug Discovery

- Improved accuracy in antibody modeling with new curated antibody database that now excludes redundant and/or poor-quality PDB structures
- Option to export all 1000 unclustered raw poses from PIPER protein docking
- Report the % humanness of the Heavy and Light chain on the grafted model in Antibody humanization by CDR grafting
- Export aggregation profile images in png format
- Report detailed patch characteristics in Protein Patch calculations
- Easily perform detailed analysis of residue scanning results with new csv file containing mutant descriptions and energies

Materials Science

GUI for Quantum ESPRESSO
Product: Quantum ESPRESSO (QE) Interface
- Convergence monitor for the nudged elastic band (NEB) calculations
- Workflow for computing dielectric constant (command line)
- Support for parallel computation of Phonon calculations (command line)
- Option to display discrete frequencies from dynamical matrix for phonon DOS
- Support for phonon calculations with Hubbard U potentials for LDA+U
- Support for mean square displacement analysis over an existing AIMD trajectory
Materials Informatics
Product: MS Informatics
- DeepAutoQSAR: Access from the Task menu under Materials Informatics
- Formulation ML: Machine-learning-based property predictions using chemical formulations
- Machine Learning Property: Improved machine learning models
- MD Descriptors: Bond, angle, torsion, and vdW energies computed as descriptors
- MD Descriptors: Improved efficiency with the MD simulation protocol
Coarse-Grained (CG) Molecular Dynamics
Product: MS CG
- CG FF Builder: Implicit charge assessment by dielectric constant
- Automated DPD Mapping: Support for multiple ionization states (command line)
- Automated DPD Mapping: Support for pre-defined patterns for use in mapping (command line)
- Support for including CGFF file (*.json) information into other CGFF files
Reactivity
Product: MS Reactivity
- Schrödinger Nanoreactor: Chemical reaction discovery and analysis module based on AIMD and semiempirical QM (xTB) methods
- Auto Reaction Workflow: Improved speed in calculating custom rates and Keq
Microkinetics
Product: MS Microkinetics
- Workflow module for microkinetic modeling of chemical reaction rates
MS Maestro Builders and Tools
- Complex Enumeration: Support for the use of two ligand libraries as input
- Complex Enumeration: Option to specify the number of unique ligands
- Move Selected Atoms: Workspace tool to rotate/translate selected atoms
Classical Mechanics
- Polymer Crosslink: Option to block formation of specific chemical structures
- Molecular Deposition: UI update with improved control of adsorbate setup and simulation protocols
Quantum Mechanics
- TST Rate: Jobs launched to queue
Education Content
- New Tutorial: Microkinetic Modeling
- New Tutorial: Machine Learning for Formulations
- New Tutorial: Nanoreactor
- New Tutorial: Modeling Receptor Binding in an Olfactory Protein
- New Tutorial: Building a Coarse-Grained Skin Model using Martini Force Field
- Updated Tutorial: Activation Energies for Reactivity in Solids and on Surfaces
- Updated Tutorial: Molecular Deposition
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.

Schrödinger Release - New Features 2024-1







At Schrödinger, we continuously strive to develop scientific solutions that push the boundaries of molecular design. We are excited to share the new features and usability improvements for Schrödinger’s 2024-1 software release—including a sneak peak of the new release of PyMOL 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.

Owner: Schrödinger, LLC
Product Name: Schrödinger Suites
Version: 2024-1 Advanced Edition *
Supported Architectures: x64
Website Home Page : www.schrodinger.com
Languages Supported: english
System Requirements: Windows & Linux **
Size: 17.0 Gb

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