Farid
Schrodinger Suites 2025 4 Windows
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 2025-4 software release.
🌟 Small Molecule Drug Discovery
🌟 Platform Environment
🌟 Maestro Graphical Interface
– One-click deletion of empty project table columns: A single menu action instantly removes all empty property columns from the entire Project Table, decluttering the workspace to allow a clearer focus on relevant data.
– “Select Entries in Table” from workspace right-click menu: Right-clicking any atom in the Workspace instantly locates and selects its corresponding entry in the Project Table, eliminating the need for manual searching in large projects.
– Maestro Assistant (Beta) enhancements: Maestro Assistant is now more interactive with the addition of a command history, copy-to-clipboard functionality, clearer mode notifications, and a streamlined feedback system.
🌟 Binding Site & Structure Analysis
🌟 SiteMap
– SiteMap now evaluates more sites than requested, returning the requested number of top-scoring sites by SiteScore
🌟 Desmond Molecular Dynamics
– Energy Decomposition Analysis panel now supports trajectories generated using custom force field parameters
🌟 Mixed Solvent MD (MxMD)
– Addition of immiscible probes in Mixed Solvent MD to better identify cryptic pockets: Use hydrophobic probes to stabilize transiently exposed pockets in an open conformation to increase their residence time and facilitate cryptic binding site identification
🌟 Ligand Preparation
🌟 Pharmacophore Modeling
– Use 1D similarities to screen against massive virtual spaces defined combinatorically with the combinatorial_explorer workflow (command line only)
🌟 Lead Optimization
🌟 Ligand alignment
– Non macrocycle alignment jobs can run as interactive tasks without submitting a job
🌟 Enumeration
– Return only Pathfinder retrosynthetic routes that include purchasable starting materials
🌟 FEP+
– Added ligand atomic RMSF analysis for RE-FEP calculations
🌟 FEP Protocol Builder
– Enable separate solvent and complex hot atom rules including None
– Enable sampling between OPLS4 and OPLS5 with the new Force Field version parameter
🌟 Quantum Mechanics
– Predict optical rotation as a function of wavelength
– Added support for 18 new double hybrid functionals
– Faster simulations with optimized CPU assignments for unbalanced batch jobs and workflows
– Employ QRNN, MPNICE and UMA MLFFs from Jaguar interfaces
🌟 Medical Chemistry Design
🌟 Ligand Designer
– Interactive Core Hopping: A new Core Swap workflow supports non-ring cores and enables true core hopping transformations, allowing for the exploration of diverse chemical space directly within an interactive design environment.
– Manual attachment point selection for macrocyclization: The newly renamed Macrocyclization workflow allows for the interactive selection of attachment points, providing precise chemical control that focuses linker enumeration on synthetically relevant designs.
🌟 De Novo Design
– New PDF report for AutoDesigner workflows to record input settings and summarize enumeration and filtering results
🌟 Drug Formulations
🌟 Crystal Structure Prediction
– Expansion of drug formulations applicability with highly accurate Z’=2 polymorph predictions (Beta): Identify stable crystal polymorphs with updated crystal structure prediction capabilities to sample, search and rank confidently
🌟 Alternative Modalities
🌟 Bifunctional Degraders
– Optionally build linkers between the two warheads in both directions when using the “Linkers only” option in the Generate Degrader Ternary Complexes interface
– Prioritize ternary complexes for linker design with a new interface to score degrader ternary complexes powered by a validated Metadynamics-based workflow (beta)
🌟 Education Content
– New Learning Path: T Cell Receptor Engineering
– New Tutorial: Enzyme Engineering with BioLuminate
– Updated Tutorial: Validating a Protein Free Energy Perturbation Model for Thermostability Predictions for Single Point Mutations (previously “Obtaining Protein Free Energy Perturbation Thermostability Predictions for Single Point Mutations”)
– Updated Tutorial: Improving the Thermostability of T4 Lysozyme Using Protein FEP+ Guided Design (previously “Introduction to Protein Thermostability Prediction using Protein FEP+”)
– Updated Tutorial: Ligand Binding Pose Generation for FEP+ (previously Ligand Binding Pose Prediction for FEP+ using Core-Constrained Docking)
– Updated Tutorial: Structure-Based Virtual Screening using Glide
🌟 Biologics Drug Discovery
– Predict T-Cell Receptor structures using TCRBuilder2 through Maestro (full release)
– Improved ability to visualize sequences before and after CDR grafting in Antibody Humanization Panel by replacing the pop-up sequence viewer with the MSV
– Streamlined visualization and plotting of mutation results by updating the mutations chart in the residue scanning results viewer interface
– Simpler analysis in the Residue Scanning Viewer by synchronization between chart and table
– In MM-GBSA Residue Scanning Viewer interface choose properties to plot on both axis, eg. plot affinity on x and stability on y-axis
– Easier setup of MM-GBSA Residue Scanning calculations through synchronization of selection between workspace and table, automatic fit-on selection, and ability to toggle visibility of select columns in property table
– New ASPmax protein descriptor capturing the maximum average surface property for aggregation propensity prediction (command line)
🌟 GUI for Quantum ESPRESSO
Product: Quantum ESPRESSO (QE) Interface
– (+DEFECT_FORMATION_ENERGY) Defect Correction: Workflow solution to compute the defect formation energy
– Upgrade to Quantum ESPRESSO 7.5
– Support for 3-body dispersion correction
– Visualization of d-band center
– Support for finite displacement phonon calculations
– Reduced disk space usage for phonon calculations
– Option to set self-consistency threshold for phonons
🌟 MS Surface
Product: MS SurfChem
– Desorption Enumeration: Active entry shown in the workspace
– Desorption Enumeration: Support for enumerating associate desorption products
🌟 Microkinetics
Product: MS Microkinetics
– Option to calculate the degree of selectivity control
– Option to plot degree of rate control per species
– Option to set pressure schedule per species
– Setup for transition state lateness parameter to define lateral interactions
– Setup for adsorbate-adsorbate interactions via lateral scaling parameter
– Support for saving and loading reaction network files
– Support for simplified reaction entry using plain text
– Support for loading a microkinetic model from a workspace entry
– Support for plotting x-axis in log scale from the viewer panel
– User control over absolute and relative error tolerances
– Number of unphysical MKM steps displayed in viewer panel
🌟 Reactivity
Product: MS Reactivity
– Nanoreactor: Option to set spin for the final state of elementary reactions
– Nanoreactor: Refined setup for metadynamics cavity radius scaled from 0.1 to 1.0
– Nanoreactor: Product chemistry filtered by refined DFT or MLFF
– Nanoreactor: Reactant energy marked in the elementary reaction network mode
– Nanoreactor: Support for MLFF (UMA) energy refinement for open shell systems
– Reaction Network Profiler: Option to sort conformers from refined energy
🌟 Advanced Force Field Applications
Product: MS FF Applications
– Expanded support for MLFF selections in QM- and MD-based workflow solutions
– UMA (developed by Meta Platforms Inc.) added as MLFF option in QM-based workflows
– (+ENABLE_GRPC_MLFF_DESMOND) UMA (developed by Meta Platforms Inc.) added as MLFF option in MD-based workflows
🌟 Transport Calculations via MD simulations
Product: MS Transport
– Ionic Conductivity: Workflow solution to predict ionic conductivity in liquid electrolyte systems
– Viscosity: Option to turn off the SHAKE algorithm (command line)
– Viscosity: Support for MLFF
🌟 Coarse-Grained (CG) Molecular Dynamics
Product: MS CG
– Coarse-grained Mapping: Consistent, reusable names for sugar particles
– Coarse-grained Mapping: Improved restraint visualization
– Coarse-grained Mapping: MARTINI mapping of proteins
– Coarse-grained Mapping: MARTINI mapping of monosaccharides
– Coarse-grained Mapping: MARTINI mapping of cholesterol
– Coarse-grained Mapping: All-atom CMS created as input for CG FF Builder
– Coarse-Grained Mapping: Enhanced precision for SMARTS patterns to improve mapping and force field parameter reusability
– Coarse-Grained Mapping: Improved UX for the reuse of existing particle types
– Coarse-Grained Mapping: Visualization of the mapped system in the workspace
– Coarse-Grained Mapping: Use of antifreeze water molecules set by default
– CG FF Builder: NpT set as the default ensemble for MARTINI simulations
– CG FF Builder: Option to keep proteins rigid during the model building stage
– CG FF Builder: Option to set the masses to standard MARTINI particle types
– CG FF Builder: Mapping of a small ion-water cluster to a single MARTINI particle
– CG FF Builder: Support for the reuse of CG particle types with identical names
– CG FF Builder: Support for loading CG mapping output as input
🌟 Complex Bilayer Builder
Product: MS Complex Bilayer Builder
– Complex Bilayer: Model building solution for complex / multi-component bilayers of molecular materials including protein-based membranes
– Membrane Analysis: Workflow solution to analyze membrane structural features
🌟 Formulation ML
Product: MS Formulation ML
– Formulation ML: Support for parallel training and predictions of multiple models
– Formulation ML Optimization: Improved UX for loading models
– Formulation ML Optimization: Option to select random optimization for models
– Formulation ML Optimization: Option to stop optimization prior to convergence
– Formulation ML Optimization: Option for cost optimization
– Formulation ML Optimization: Support for composition constraints with Bayesian optimization
– ML Model Manager: Option to export and update descriptors for ingredients
– ML Model Manager: Automatic selection for the newly loaded model
– ML Model Manager: Access for model names to be edited by user
– ML Model Manager: Option to estimate MPO scores on model predictions
🌟 Layered Device ML
Product: MS Layered Device ML
– OLED Device ML: Advanced options for model training
– OLED Device ML: Option to export the training set data
– OLED Device ML: Support for parallel training and predictions of multiple models
– OLED Device ML: Option to use molecular model predictions as descriptors
🌟 MS Maestro User Interface
– Maestro: Job Monitor to display the cause of failures for failed jobs
– Maestro: Ribbon style enabled in the workspace for protein representations
🌟 MS Maestro Builders and Tools
– Complex Builder: Option to turn on/off IUPAC name assignment for ligands
– Complex Builder: Support for building dimers with an atom bridging two metals
– Disordered System: Preservation of protein residue information by default
– Disordered System: Option to set the system size by the total number of atoms
– Materials Science Panel Explorer: GUI to search and list panels by the application, method, chemistry, and product of interest
– Meta Workflows: Matched settings for the Brownie stage with the MD Multistage
– Optoelectronic Device Designer: Option to import materials data from a file
– Optoelectronic Device Designer: Option to export materials and device data
– Optoelectronic Device Designer: Option to remove materials from the database
– Optoelectronic Device Designer: Plot for numerical energy levels
– Optoelectronic Device Designer: Plot for numerical layer thicknesses
– Solvate System: Option to specify particle radii for coarse-grained models
– Solvate System, Structured Liquid GUI: (+MATSCI_PACKMOL_PBC) Periodic boundary conditions retained when building structures
🌟 Classical Mechanics
– Cluster Analysis: (+CLUSTER_DENSITY_PROFILE) Radial density profile for clusters
– Evaporation: Support for MLFF
– Evaporation: Setup for evaporation zone in radial distance from center of mass
– Polymer Crosslink: (+POLYMER_CROSSLINK_MODES) Option to select fast crosslinking mode
– Thin Plane Shear: Support for MLFF
– Thin Plane Shear: Option to use custom MLFF
– Umbrella Sampling: User control over potential of mean force (PMF) calculations
– Umbrella Sampling: Visualization of probability distribution overlap matrix
– Visualize Restraints: Visualization of multiple restraints
🌟 Quantum Mechanics
– Adsorption Site Finder: Support for MLFF
– Bond and Ligand Dissociation: Support for MLFF
– QM Multistage: Support for MLFF selection on the Theory tab
– Optoelectronic Film Properties: Advanced transition dipole moment analysis with distributions over angle, distance, and depth
– Probe Grid Scan: VdW radius used as atomic radius for metal atoms
– Probe Grid Scan: Support for scanning open shell systems using MLFF (UMA)
🌟 Education Content
– New Tutorial: Simulating Complex Protein Solutions
– New Tutorial: Creating a Coarse-Grained Model for Protein Formulations
– New Tutorial: Building and Analyzing a Complex Lipid Bilayer and Embedding a Membrane Protein
– New Tutorial: Ionic Conductivity
– New Tutorial: Optimizing Viscosity and Cost in Formulations with Missing Structural Data
– New Tutorial: Locating Adsorption Sites on Surfaces
– Updated Tutorial: Atomic Layer Deposition
– Updated Tutorial: Microkinetic Modeling
– Quick Reference Sheet: Materials Science Panel Explorer
🌟 Education Content
🌟 Life Science
– New Learning Path: T Cell Receptor Engineering
– New Tutorial: Enzyme Engineering with BioLuminate
– Updated Tutorial: Validating a Protein Free Energy Perturbation Model for Thermostability Predictions for Single Point Mutations (previously “Obtaining Protein Free Energy Perturbation Thermostability Predictions for Single Point Mutations”)
– Updated Tutorial: Improving the Thermostability of T4 Lysozyme Using Protein FEP+ Guided Design (previously “Introduction to Protein Thermostability Prediction using Protein FEP+”)
– Updated Tutorial: Ligand Binding Pose Generation for FEP+ (previously Ligand Binding Pose Prediction for FEP+ using Core-Constrained Docking)
– Updated Tutorial: Structure-Based Virtual Screening using Glide
🌟 Materials Science
– New Tutorial: Simulating Complex Protein Solutions
– New Tutorial: Creating a Coarse-Grained Model for Protein Formulations
– New Tutorial: Building and Analyzing a Complex Lipid Bilayer and Embedding a Membrane Protein
– New Tutorial: Ionic Conductivity
– New Tutorial: Optimizing Viscosity and Cost in Formulations with Missing Structural Data
– New Tutorial: Locating Adsorption Sites on Surfaces
– Updated Tutorial: Atomic Layer Deposition
– Updated Tutorial: Microkinetic Modeling
– Quick Reference Sheet: Materials Science Panel Explorer
🌟 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 2025-4 | Life Science – New Features
Schrödinger Release 2025-4 | Materials Science – New Features
🌟 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: 2025-4 Commercial Version *
🌟 Supported Architectures: x64
🌟 Website Home Page :
http://www.schrodinger.com
🌟 Languages Supported: english
🌟 System Requirements: Windows, Linux, macOs **
🌟 Size: 32.9 Gb
* Notes: All workflows that rely on Desmond are not supported on Windows or Mac platforms, they can only be run on Linux. This includes Molecular Dynamics, IFD-MD, FEP+, WaterMap, and a number of Materials Science workflows. GPU machine learning applications such as Active Learning Glide and DeepAutoQSAR on GPU can only be run on Linux.
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⭐️ Schrodinger Suites 2025 4 Windows – (8.65 GB)
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