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Free Download Schrodinger Suites 2025-4 | 32.9 Gb

Owner:Schrödinger, LLC

Product Name:Schrödinger Suites

Version:2025-4 Commercial Version *

Supported Architectures:x64

Website Home Page :www.schrodinger.com (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.

Updated: Added Schrodinger_Suites_2025-4_Documentation

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 2025-4software 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 Descriptionting 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 Description on both axis, eg. Description 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 Description 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 Descriptionting 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: Description for numerical energy levels

- Optoelectronic Device Designer: Description 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

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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 2025-4 | Life Science - New Features

Schrödinger Release 2025-4 | Materials Science - New Features

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.

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