All Schrödinger offices worldwide will be closed for the week of August 17-21 as part of a company-wide initiative to rest and recharge. Please expect limited responses during this time. Scientific and Technical Support team members will be available to answer emergency support issues only.

AI in Drug Discovery 2025

Conference

AI in Drug Discovery 2025

CalendarDate & Time
  • March 10th-11th, 2025
LocationLocation
  • London, United Kingdom

Schrödinger is excited to be participating in the AI in Drug Discovery 2025 conference taking place on March 10th – 11th in London, United Kingdom. Join us for a presentation by Sathesh Bhat, Executive Director of Schrödinger Therapeutics Group, titled “Advancing drug discovery programs with machine learning-enhanced in silico design.” Stop by our booth to speak with Schrödinger scientists.

icon time MAR 10 | 11:00AM CET
Advancing drug discovery programs with machine learning-enhanced in silico design

Speaker:
Sathesh Bhat, Executive Director, Schrödinger Therapeutics Group

Abstract:
Recent advances in integrating machine learning and physics-based calculations have transformed pre-clinical drug discovery. In this presentation, we demonstrate how large-scale de novo design workflows dramatically accelerated an EGFR discovery project, enabling the exploration of 23 billion designs and identification of four novel scaffolds with favorable potency and property profiles in just six days. We also showcase the application of de novo core design strategies to develop selective scaffolds targeting WEE1, where our automated approaches generated novel chemotypes achieving >10,000x selectivity over PLK1 while maintaining potent target inhibition. Finally, we introduce FEP+ Protocol Builder, representing a new paradigm in combining machine learning with physics-based methods. This system uses active learning to systematically optimize free energy perturbation protocols, automating what has traditionally been a manual, expertise-driven process. Integrating machine learning with rigorous physics-based calculations exemplifies how hybrid computational approaches can provide both speed and accuracy in modern drug discovery.

Display Week 2025

Conference

Display Week 2025

CalendarDate & Time
  • May 11th-16th, 2025
LocationLocation
  • San Jose, California

Schrödinger is excited to be participating in the Display Week 2025 conference taking place on May 11th – 16th in San Jose, California. Join us for a presentation in the Exhibitor Forum by Hadi Abroshan, Product Manager of Organic Electronics at Schrödinger titled, “Revolutionizing Display Technology: Digital Solutions from Materials to Devices.” Stop by booth 1532 to speak with Schrödinger scientists.

icon time MAY 14 | 9:15AM
Revolutionizing Display Technology: Digital Solutions from Materials to Devices

Speaker:
Hadi Abroshan, Product Manager of Organic Electronics, Schrödinger

Abstract:
Digital solutions are transforming display technology by accelerating materials discovery and device optimization. Advanced simulations, AI/machine learning, and cloud-based tools drive faster innovation in OLEDs, MicroLEDs, and beyond—enhancing efficiency and lifetime while reducing costs from materials to final devices. We will present the latest computational technologies and also showcase a synergistic application of Ansys and Schrödinger predictive technologies to accelerate OLED development through a multi-scale, multi-physics simulation approach.

Device Packaging 2025

Conference

Device Packaging 2025

CalendarDate & Time
  • March 3rd-6th, 2025
LocationLocation
  • Phoenix, Arizona

Schrödinger is excited to be participating in the Device Packaging 2025 conference taking place on March 3rd – 6th in Phoenix, Arizona. Join our poster and collaborated talk with Samsung. Stop by booth #704 to speak with us.

icon time MAR 5 | 5:30 PM
Poster: Materials innovation for advanced electronic packaging using digital chemistry

Speaker:
Atif Afzal, Principal Scientist II, Schrödinger

Abstract:
The push for ever-improving characteristics of electronic devices demands packaging materials with superior thermal stability, mechanical strength, water repellency, and interfacial properties. Traditional material selection methods, often reliant on extensive empirical testing, are time-consuming and costly, limiting the ability for researchers to push beyond what they already know. To address these challenges, we propose a new approach that integrates physics-based modeling with machine learning (ML) to accurately model and predict the properties of advanced materials for electronic packaging. Our physics-based modeling, molecular dynamics (MD) simulations, offer detailed atomistic insights into material behavior under various conditions, providing essential data on thermal properties, mechanical resilience, adhesion, and more. To accelerate the material evaluation process and to navigate new chemical domains more efficiently, we integrate ML in our workflows. By training ML models using both experiment and simulation data, we can rapidly predict the properties of new materials, enabling efficient screening and selection. We demonstrate the efficacy of this approach through a case study focused on designing copolymers with targeted properties. Our integrated MD-ML framework allows us to quickly identify polymers that meet specific performance criteria, such as enhanced glass transition and superior dielectric properties, while significantly reducing the time and resources required for material discovery. This work highlights the transformative potential of combining physics-based simulations with machine learning in the field of electronic packaging. By streamlining the material development process, our approach not only accelerates innovation but also enables the creation of materials that meet the stringent demands of next-generation electronic devices.

icon time MAR 5 | 2:00 PM
Talk: Material property simulation for advanced packaging

Speaker:
Seo Young, Samsung; Atif Afzal, Schrödinger

Abstract:
Advanced packaging allows chiplet integration and maximizes device performance with faster product development cycle, lower cost, and higher yield. As the package size becomes bigger and the device is getting more complicated, there is growing motivation to employ manufacturing process simulation, Artificial Intelligence (AI) assisted process optimization, yield and reliability prediction, rather than conventional methods, to ramp the yield and to ensure the reliability of a new product. The key for an accurate process simulation model is to input precise material properties, such as modulus, Coefficient of Thermal Expansion (CTE), dielectric constant, glass transition temperature, etc., which could change non-linearly with temperature, moisture, as well as other environmental factors and process conditions. Molecular modeling and molecular dynamics can provide insights into post chemical reactions or physical transformations via atomic and molecular simulations. Lithography Techniques for Redistribution Layer (RDL) fabrication are the foundation of Advanced Packaging techniques, such as Fan Out Wafer Level Packaging (FOWLP), Fan Out Panel Level Packaging (FOPLP), 2.5D, 3D, and 3.5D packaging with RDL interposers. The continuous scaling-down of critical dimensions (CDs) in advanced packages, including via diameters, routing line and space (L/S), to a few microns, or submicron level, as well as the increasing number of RDL layers at panel scale pose significant challenges in RDL lithography techniques. For example, the Photo Imageable Dielectric (PID) or other build-up dielectric materials used in multilayer RDL fabrication are polymers, having low Young’s modulus, high CTE, and big volume shrinkage after curing. These material properties could cause fabrication process induced warpage and surface topography deformations, such as non-planarity, roughness, contamination, defects, and dimensional variations, which could potentially lead to massive yield loss when forming fine features during the multilayer RDL patterning. This paper presents material simulation methodologies based on quantum mechanics (QM), molecular dynamics (MD), and Machine Learning (ML), which are adopted to predict the material properties of a PID material, including glass transition temperature (Tg), CTE, mechanical properties, dielectric properties, as well as volume shrinkage after curing. Comparison between the simulation results and the experimental data is performed to validate the methodology. Similar methodology could be used to predict material properties of other organic packaging materials, which is crucial for building up accurate process, yield, and reliability simulation or digital twin of advanced packaging.

JEC World 2025

Conference

JEC World 2025

CalendarDate & Time
  • March 4th-6th, 2025
LocationLocation
  • Paris, France

Schrödinger is excited to be participating in the JEC World 2025 conference taking place on March 4th – 6th in Paris, France. Join us for a presentation by Andrea Browning, Director at Schrödinger, titled, “Implementing AI along the Composites Value Chain.” Stop by booth #5K132 to speak with us.

icon time MAR 6 | 12:00
icon location Agora 5
Implementing AI along the Composites Value Chain

Speaker:
Andrea Browning, Director, Schrödinger

Abstract:
The composites industry is poised for a groundbreaking transformation fueled by the recent surge in material data and computational power. This session dives deep into the exciting possibilities of Artificial Intelligence and Machine Learning (AI/ML) along the entire composites value chain. We’ll explore how AI can revolutionize every step, from the development of innovative composite materials to optimizing their design, selection, and certification. Discover how AI can streamline manufacturing processes, boost production efficiency, and even monitor the structural health of composites in real-time. Witness how this powerful technology is paving the way for a new era of intelligent composites manufacturing.

LOPEC 2025

Conference

LOPEC 2025

CalendarDate & Time
  • February 25th-27th, 2025
LocationLocation
  • Munich, Germany

Schrödinger is excited to be participating in the LOPEC 2025 taking place on February 25th – 27th in Munich, Germany. Join us for a presentation by Hadi Abroshan, Principal Scientist at Schrödinger, titled “Integrating Atomistic Simulations, Machine Learning, and Cloud-Based Collaboration for Next-Generation Electronic Materials.” Stop by booth #B0313 to speak with Schrödinger scientists.

Click here to learn how Schrödinger’s digital chemistry platform empowers you to discover novel optoelectronics materials.

icon time FEB 26 | 15:20 CET
icon location Room 2
Integrating Atomistic Simulations, Machine Learning, and Cloud-Based Collaboration for Next-Generation Electronic Materials

Speaker:
Hadi Abroshan, Principal Scientist, Schrödinger

Abstract:
The creation of next-generation display technologies hinges on innovative research strategies and collaborative tools. This presentation highlights how the integration of physics-based simulations, machine learning (ML), and a cloud-enabled platform accelerates the discovery and refinement of advanced optoelectronic materials. We introduce the Schrödinger digital chemistry platform, which facilitates advanced simulations of optoelectronic materials, spanning from individual molecules to thin films developed via vacuum deposition or solution processing. This platform’s automated capabilities predict key material properties such as electronic transitions, hyperfluorescence, charge carrier mobility, refractive index, thermophysics, interfacial mixing, and molecular orientation. We then explore the synergy between physics-based simulations and ML, which significantly streamlines the materials discovery process. By analyzing large datasets and identifying trends, ML allows for faster predictions of material properties. An active learning screening process efficiently pinpoints promising candidates based on multiple properties, all while reducing computational cost. Further, we discuss genetic optimization algorithms that drive the development of new materials for electroluminescent devices. These algorithms emulate natural selection, refining material properties iteratively to uncover high-performance compounds tailored to specific targets. When combined with high-throughput screening, this approach accelerates the exploration of chemical space, leading to rapid material advancement. Lastly, we introduce Schrödinger’s LiveDesign, a web-based collaboration platform that enhances modern R&D by integrating advanced modeling, data management, and ideation. LiveDesign empowers research teams to collaborate effectively, regardless of geographic location, supporting a seamless end-to-end research workflow.

SCC78 2024

Conference

SCC78 2024

CalendarDate & Time
  • December 11th-13th, 2024
LocationLocation
  • Los Angeles, California

Schrödinger is excited to be participating in the SCC78 conference taking place on December 11th – 13th in Los Angeles, California. Join us for a presentation by Haidong Liu, Senior Scientist at Schrödinger, titled “Screening Antioxidant Ingredients Using Machine Learning and Physics-based Modeling .”

icon time DEC 12 | 3:30 PM
icon location Session G: AI Beauty Revolution
Screening Antioxidant Ingredients Using Machine Learning and Physics-based Modeling 

Speaker:
Haidong Liu, Senior Scientist, Schrödinger

Abstract:
Antioxidants are an important ingredient for cosmetic products to alleviate oxidative stress. While high-throughput screening for new antioxidant candidates still remains challenging experimentally. And the data-driven machine learning models would require the input of a reliable dataset. Here we present an efficient computational approach that combines the physics-based and machine learning tools to address this issue, and this approach only uses molecular structures as inputs.

We used molecular quantum mechanical (QM) calculation and machine learning to predict the antioxidant activity through hydrogen atom transfer (HAT) mechanism. We first constructed a library of flavonoid structures and then calculated the hydrogen dissociation energies of the hydroxyl group in solvents using QM. The machine learning model was trained and validated using the hydrogen dissociation energies from QM calculations. We can easily screen thousands of molecules, and this physics-based and machine learning combined approach can be used for other properties.

MRS Fall 2024

Conference

MRS Fall 2024

CalendarDate & Time
  • December 1st-6th, 2024
LocationLocation
  • Boston, Massachusetts

Schrödinger is excited to be participating in the MRS Fall 2024 conference taking place on December 1st – 6th in Boston, Massachusetts. Join us for presentations by Schrödinger scientists on Dec 4th and 5th. Additionally, attend a presentation on Dec 3rd by Panasonic, co-authored by Schrödinger, titled “Discovering Low-Viscosity Molecules Using an Integrated Physics-Based Modeling, High-Throughput Screening, and Active Learning Approach (2)— Screening from PubChem Database.”

 

icon time DEC 3 | 8:00 PM
icon location Hynes, Level 1, Hall A
Discovering Low-Viscosity Molecules Using an Integrated Physics-Based Modeling, High-Throughput Screening, and Active Learning Approach (2)— Screening from PubChem Database

Presenters:
Nobuyuki Matsuzawa, Hiroyuki Maeshima, Tatsuhito Ando, Atif Afzal, Benjamin Coscia, Andrea Browning, Mathew Halls, Karl Leswing, Tsuguo Morisato

Schrödinger collaborated with Panasonic on this presentation

icon time DEC 4 | 3:45 PM
icon location Hynes, Level 3, Ballroom C
Discovering Low-Viscosity Molecules Using an Integrated Physics-Based Modeling, High-Throughput Screening and Active Learning Approach (1)— Screening from the GDB Database

Speaker:
Atif Afzal, Principal Scientist

Abstract:
The discovery of low-viscosity molecules is crucial for the development of next-generation batteries and capacitors. Large molecular libraries available in the literature provide a valuable resource for identifying promising candidates. In this study, we utilized the GDB database1, one of the largest repositories of small molecules, to identify low-viscosity molecules. We employed and benchmarked molecular dynamics methods to accurately compute the dynamic properties without the need for synthesis or empirical testing, validating our calculations against experimental data. However, the number of molecules of interest from the GDB database is too large (several hundreds of thousands), making it impractical to identify promising candidates using purely physics-based models due to computational costs. Therefore, we implemented advanced machine learning (ML) techniques and smart selection approaches to dramatically reduce the number of physics-based calculations needed. Physics-based simulations of viscosity included both Green-Kubo and Einstein-Helfand approaches allowing for robust calculation across the selected molecules. By employing an active learning approach, we optimized the selection of molecules, enhancing the efficiency of the ML model while targeting low-viscosity candidates. Additionally, we computed the boiling points (BP) of the molecules using ML models trained on experimental BP data. As a result, we identified more than 100 molecules with viscosities less than 0.35 cP and BP above 80°C. We demonstrate that by integrating accurate physics-based models with advanced ML techniques, we can effectively identify top molecular candidates while significantly reducing computational costs.

icon time DEC 5 | 11:15 AM
icon location Sheraton, Second Floor, Constitution B
Prediction of aqueous and non-aqueous solubility using machine learning

Speaker:
Lihua Chen, Senior Scientist

Abstract:
Solubility, the capacity of a solute to dissolve in a solvent, forming a solution, is a crucial design parameter across various materials and life science applications. Due to the high cost of experimental measurements, we have developed quantitative structure-property relationship (QSPR) models to rapidly and accurately predict aqueous solubility in water and non-aqueous solubility in organic solvents. For this purpose, we gathered 14,485 room temperature aqueous solubility data points and 45,313 temperature-dependent non-aqueous solubility data points from literature and open-source databases. Additionally, we incorporated advanced cheminformatics-based, graph-based, and physics-based descriptors computed through classical molecular dynamics to optimize machine learning performance. These models can significantly streamline molecular discovery by providing rapid, accurate solubility predictions, reducing the need for costly experiments, and accelerating the identification and optimization of promising candidates.

Release 2024-4

Library Background

Release Notes

Release 2024-4

Small Molecule Drug Discovery

Platform Environment

Maestro Graphical Interface

  • Improved usability in scatter plots and histograms:
    • See relationships in data across multiple plots and histograms with streamlined menu into “Entry Actions” and “Sync Options” menu icon
    • Added support for string and boolean histograms
  • In the histogram panel, easily switch between settings and data table views
  • Specify the number of columns and rows for fine control of Workspace Tiles
  • Save animated GIF of vibrational motion from Jaguar frequency calculation
  • Enhanced Cryo-EM surface performance:
    • Up to 2x faster loading of Cryo-EM surface files
    • Up to 5x increase in speed for isosurface contour creation and adjustments
  • Refined toolbar design for enhanced simplicity, modern aesthetics, and optimization for dark mode
  • Updated Maestro Project format to version 5:
    • Support for multi-letter chain names beyond traditional 26 characters
    • Compressed .prjzip files designed for easy sharing via email
    • Automatic conversion of version 4 projects to version 5 upon opening
    • By default save Maestro Projects in version 5 format with an option to save in version 4 for backward compatibility
  • Support added for two new CIF file formats: “PDBx/mmCIF (*.cif)” and “Small Molecule CIF (.cif)”
  • Opening Maestro locally from LiveDesign is now supported on macOS, Linux, and Windows
  • Revamped splash screens & iconography: Modern visuals for an updated look and feel

Workflows & Pipelining [KNIME Extensions]

  • LiveDesign Admin node can take user credentials from the LiveDesign Connection node enabling SSO configuration

Target Validation & Structure Enablement

Protein Preparation

  • Protein The Protein Preparation Workflow now considers Epik states of ligands during the hydrogen-bond network optimization stage by default

Protein X-Ray Refinement

  • New sf2map.py script quickly generates an aligned x-ray map, given an input structure and a cif file containing structure factors

IFD-MD

  • Updated IFD-MD for automatic sampling of histidine tautomer states (HID, HIE): Consider induced fit effects simultaneously to resolve receptor tautomeric states and predict receptor and ligand conformations

Binding Site & Structure Analysis

SiteMap

  • Automatically apply Combined Mode which breaks down sites larger than 800 Å3

Mixed Solvent MD (MxMD)

  • Improved cryptic pocket identification with new mixed solvent molecular dynamics (MxMD) interface including customizable visualization (Beta): Gain a clearer understanding of candidate binding pockets on the protein surface with a new interface to set up and analyze MxMD simulations

Hit Discovery

Active Learning Applications

  • Faster time-to-results in AL-Glide and Glide using ZeroMQ mode for machine learning evaluation stage and Glide docking stage

Shape Screening

  • Additional similarity normalization schemes now available for Quick Shape and 1D Screening command. In addition to the max{O(A,A), O(B,B)} default can apply min{O(A,A), O(B,B)}, O(A,A), and O(B,B) where O(A,B) is the overlap between ligands A and B
  • Run Quick Shape and 1D Screens against a Phase pharmacophore hypothesis as the query
  • Improve speed of Quick Shape calculations with -limit and -NJOBS1D options that enable more efficient utilization of compute resources

Glide

  • Full release of Glide WS mode, previously known as WScore, to prioritize ligands for improved hit enrichment and pose prediction accuracy
    • Leverages explicit water energetics to enhance the accuracy of protein-ligand poses and reduce experimentally inactive compounds in top-scoring virtual hits

Lead Optimization

FEP+

  • Gain deeper insights into receptor-ligand interactions with new Per-Residue Energy Decomposition in FEP Edge analysis
  • Perform categorical analysis in the Correlation Plot (FEP+) interface using classification matrices including common metrics such as Accuracy, Specificity, Recall, Precision, F1 Score, Cohen’s K and Kendall’s T
  • View reason why compounds are skipped in ABFEP calculations in the FEP+ Panel

Protein FEP+

  • Full release of Protein FEP+ Residue Scanning (with lambda dynamics)
    • Workflow now generates an FMP archive to be loaded in the FEP+ Panel
    • Web Services support

FEP+ Protocol Builder

  • Ability to run with either OPLS4 or OPLS5 force field
  • Added support for sampling of more residue protonation states
  • New option to skip active learning and perform exhaustive exploration of protocol parameter space

Quantum Mechanics

  • Return solvation entropy in implicit solvent calculations
    distributed_frequencies.py workflow for numerical frequency calculations
  • Added support for isotope 11B in NMR calculations
  • Implicit solvent model SMD now has gradients and frequencies
  • E-sol now supports the CPCM-X implicit solvation method for rapid solvation energies (command line only)

Semi-Empirical Quantum Mechanics

  • Updated xTB to version 6.7.1 which uses the advanced solvent model CPCM-X

Macrocycles

  • Expanded list of predefined linkers from 5 to 22 for small molecule cyclization in macrocycle.py
  • Expanded list of side-chain bridges for peptide cyclization from 4 to 21 of the most commonly reported in the literature
  • Control spacers in macrocyclize.py via a CSV file of SMILES strings
  • Improvements to macrocycle alignment reproducibility and performance in tug_align script and Ligand Alignment Panel
  • Macrocycle sampling script can optionally output only macrocycle conformers
  • Easily create cyclic peptides from sequence on the command line with peptide_cyclize.py script

De Novo Design

AutoDesigner – R-group Design

  • Boost exploration of similar ligands with new AutoDesigner Similarity feature that scores output ideas based on similarity to a user-provided set of compounds
  • Added exhaustive PathFinder enumeration of all routes of the starting ligand using all available building blocks for those routes
  • Added recursive trimming of the final set of outputs to generate additional outputs
  • Improved logging including an overview of the number of compounds generated at various stages of the workflow

AutoDesigner – Core Design

  • Improved logging including an overview of the number of compounds generated at various stages of the workflow

Biologics Drug Discovery

  • Predict protein properties with automated machine learning model building using protein descriptors: Leverage AutoQSAR analysis to train, validate, and apply AI/ML models for biologics properties prediction
  • Predefined selection sets for quick access to TCR regions like CDRs, alpha/beta chains, and more

Materials Science

GUI for Quantum ESPRESSO

Product: Quantum ESPRESSO (QE) Interface

  • Phonon-dependent dielectric properties reported in the Phonon DOS viewer
  • Workflow action menu (WAM) for NMR calculations
  • Support for phonon calculations with DFT-D3
  • Improved cell relaxation protocol
  • Schrödinger-compatible Quantum ESPRESSO releases available at Github
  • Support for distributed phonon calculations
  • Control over maximum number of retries after failure via config file (command line)
  • Initial parameters and constraints preserved in the QM Convergence Monitor

KMC Charge Mobility

Product: MS Mobility

  • Compute KMC Charge Mobility: Improved speed with robust QM convergence (command line)

Materials Informatics

Product: MS Informatics

  • Formulation ML: Increased number of available steps for hyperparameter tuning
  • Formulation ML: Option to replace hyperparameter tuning steps with training time
  • Formulation ML: Visualization of atomic contributions from the feature importance analysis
  • Machine Learning Property: Updates to existing models
  • Machine Learning Property: Prediction of melting point for molecular solids
  • Machine Learning Property: Prediction of non-aqueous solubility of molecules

Coarse-Grained (CG) Molecular Dynamics

Product: MS CG

  • Automated CG Mapping: Speed up for mapping large molecules
  • Automated CG Mapping: Particle types and the number of occurrences reported

Penetrant loading simulations

Product: Penetrant Loading (PL)

  • Penetrant Loading: Differentiation between pre-existing water and added water

Reactivity

Product: MS Reactivity

  • Nanoreactor: Option to set the width of the biasing potential
  • Reaction Workflow: Anharmonic zero point energy (ZPE) added to Project Table
  • Reaction Workflow: Support for enumeration on sites in rings
  • Reaction Workflow: Option to automate the swap fragment with enumeration
  • Reaction Workflow: Preview of reaction diagram at the setup

Microkinetics

Product: MS Microkinetics

  • Microkinetic Modeling: Support for multistage MKM analysis
  • Microkinetic Modeling: Support for zoom in on plots in the viewer panel
  • Microkinetic Modeling: Increased default value for maximum integration time step

MS Maestro Builders and Tools

  • Adsorption Enumeration: Support for selection of reactive atoms by atom indices
  • Disordered System: Improved UI with reconfigured options for tabs and dialogs
  • Disordered System: Support for keeping selected molecules rigid with tangled-chain option
  • Meta Workflows: Support for radial distribution function analysis
  • Nanoparticle: Option to include only molecules with center of mass inside the particle

Classical Mechanics

  • Barrier Potential for MD: Option to remove barrier from input structures
  • Droplet: Support for entering random seed in building a droplet
  • Droplet: Support for randomized initial velocities
  • Evaporation: Support for full control over which profiles to plot
  • Evaporation: Support for applying barrier potentials
  • Evaporation: Option to set evaporation zone based on the distance from COM of the substrate
  • Evaporation: Improved loading speed for large input structures
  • MD Multistage: Improved relaxation protocol for ladder polymers
  • Refined default timestep for DPD particles
  • Thermostat and barostat settings set automatically for atomistic and coarse-grained systems
  • Stress Strain: Option to plot normal average stress
  • Thermophysical Properties: Option to return *.ene files (command line)
  • Trajectory Density Analysis: Output *.csv files

Quantum Mechanics

  • Adsorption Energy: Option to select between kcal/mol and kJ/mol for energy units
  • Adsorption Energy: All output entries incorporated in Project Table as subgroups
  • Adsorption Energy: Robust detection algorithm for valid input adsorbates
  • Adsorption Energy: Support for loading options from a Quantum ESPRESSO config file
  • Optoelectronic Film Properties: Prediction of molecular refractive indices
  • Optoelectronic Film Properties: Prediction of intersystem and reverse intersystem crossing rates
  • Optoelectronic Film Properties: Improved loading protocols for large input structures

Education Content

Life Science

  • New Tutorial: Protein pKa Prediction with Constant pH Molecular Dynamics
  • Updated Tutorial: Glide WS Evaluation of HSP90 Ligands

Materials Science

  • New Tutorial: Singlet-Triplet Intersystem Crossing Rate
  • New Tutorial: Modeling the Formation and Decomposition of Nitrosamines
  • New Tutorial: Atomic Layer Deposition
  • New Tutorial: Elemental Enumeration
  • New Quick Reference Sheet: Refractive Index
  • Updated Tutorial: Introduction to Multistage Quantum Mechanical Workflows

Docs Content

  • New documentation page to explore solutions for materials science applications and to identify the best fit for users’ interest
  • Panel images shown in the help topic of each panel

LiveDesign

What’s new in 2024-4

  • Biologics SAR Visualization: View, highlight, and analyze properties alongside sequence differences in the Sequence Viewer tool
  • Ligand Designer
    • Upload multiple overlays in the Ligand Designer Configurations via the admin panel, and enable or disable the overlays during design sessions
    • Rename ligands after editing and using the “predict pose” functionality to track and manage iterative design changes
  • R-group enumeration: Filter output products by computed properties
  • LiveDesign Learning: View the LiveDesign Learning Dashboard within Landing Pages
    • *LiveDesign Learning is now called LiveDesign ML

  • LiveReport Management
    • View row, column, and cell count for LiveReports in the LiveReport Picker
    • Set up a LiveReport as Read-Only or Hidden during creation in an updated Create LiveReport dialog
    • The following menu items have been consolidated into an “Edit LiveReport…” menu: Rename, Move to Folder, Make Read Only and Make Editable, Make Hidden and Make Visible
    • Admins can update Read-Only LiveReports to make them editable
    • Unhide a subset of compounds by clicking on a link in the LiveReport footer and selecting the compound IDs in a dialog
  • Documentation
    • The ? button in LiveDesign now directs to online documentation as is done elsewhere in the Schrödinger platform. Users will be directed to log into their Schrödinger web account that will be verified with a code to their email; if they do not have a web account, they will need to sign up for one.
  • Copy values from the Form spreadsheet, table, and ID widgets to the clipboard
  • Search and filter for a column name in the Create MPO dialog when adding a constituent column from the LiveReport
  • Click a link in a 3D cell for a 3D Generic Entity and Explicit Ligand Designer to view the 3D structure in Maestro
  • Entities appear in a LiveReport more quickly after a reaction enumeration, R-group enumeration, file upload, Maestro upload, and LDClient upload
  • LDClient’s API for retrieving FFC columns “get_freefrom_column_by_id” will now include an “updated_at” field containing a long corresponding to the timestamp that the FFC was last updated
  • Landing Page: View recent published experimental data from the Compound’s Page

What’s Been Fixed

  • Adding an entity to an Advanced Search, by searching for its ID, would show an unresponsive dialog, and now shows a dialog that accept an ID.
  • Complex filters would not accept a pasted biologic sequence, and would fail to filter to that sequence, but now accept pasted biologic sequences.
  • Creating a LiveReport from a template in the Landing Page would not open the newly created LiveReport, and now opens the LiveReport in a new browser tab.
  • If an entity is imported to multiple projects, purging the entity from one of the projects will make it disappear from that project only. Only one file entry now appears in the Manage Files Dialog for a multi-entity import through CSV, ZIP, and FASTA.
  • String type of entity relationship metadata is supported in DI by adding a DI mapping for relationship and relationship metadata.
  • The column “Structure Class” has been renamed to “Entity Type” in the Data & Columns tree
  • Pasting aromatic structures into the sketcher would flip chirality on structures containing a pyrrole, and now the chirality is maintained.
  • When entering FFC date values via LDClient, users must now use the YYYY-MM-DD format. If the date is entered in an incorrect format, the system will return a 400 error with the message: ‘Date must be in YYYY-MM-DD format.’
  • Forms kanban widgets would show a pin icon beside the kanban tile, and now pin icon does not appear in kanban widgets.
  • Unpinning a row now works as expected.
  • Model results with multiple values in a cell would show a different order of values if the LiveReport was duplicated, and now show the same order in the duplicated LiveReport as the origin LiveReport.
  • The Guanidine group in Arginine incorrectly displayed a carbon with five bonds in the 3D visualizer, and now accurately represents the chemistry, showing the correct bonding structure for Arginine residues.
  • Reordering of R-group scaffolds will work for newly added or deleted scaffold without page refresh in SAR analysis(R-group decomposition).
  • The deleted docked poses will no longer reappear, ensuring a clean and organized workspace. Each new pose generated after clicking “predict pose” will be sequentially named, allowing for easy tracking (e.g., “docked_ligand_4” following the deletion of “docked_ligand_3”).
  • Changing the model’s name via Admin panel will get correctly reflected in the Ligand Designer.
  • Targets would remain visible in the 3D visualizer after unchecking the display checkbox and then selecting a different entity, and now the Target display checkbox remains unchecked and the Target is not visible.
  • Copying a LiveReport from one project to another would grant the destination project ACLs to any model within the LiveReport, even if the Model’s Protocol did not provide access to the destination project. Now, the model column will be “dummified” and not visible in the destination project if the Protocol does not provide access to that project.
  • Models with dependent parameterized models will not show an error when archived, and all of its dependent parameterized models will also get archived. A dialog box will appear stating the number of dependent parameterized models that will be archived.

Training & Resources

Online Certification Courses

Level up your skill set with hands-on, online molecular modeling courses. These self-paced courses cover a range of scientific topics and include access to Schrödinger software and support.

Tutorials

Learn how to deploy the technology and best practices of Schrödinger software for your project success. Find training resources, tutorials, quick start guides, videos, and more.

Other Resources

AI in Drug Discovery USA 2024

Conference

AI in Drug Discovery USA

CalendarDate & Time
  • October 21st-22nd, 2024
LocationLocation
  • Boston, Massachusetts

Schrödinger is excited to be participating in the AI in Drug Discovery USA conference taking place on October 21st – 22nd in Boston, Massachusetts. Join us for a presentation by Karl Leswing, Executive Director, Machine Learning at Schrödinger, titled “Latest advancements in machine learning-enhanced in silico design: Impact on a pipeline of drug discovery programs.”

Speaker:

Karl Leswing, Executive Director, Machine Learning, Schrödinger

Key Learning Objectives:

  • Using active learning with FEP+ for large-scale in silico fragment screens in hit discovery
  • Applying de novo design workflows for intelligent molecular core design
  • Leveraging experimental data for enhancing ADMET profiles in lead optimization using an interactive ML dashboard

Karl Leswing

Executive Director, Machine Learning, Schrödinger

Karl Leswing is the Executive Director for Machine Learning at Schrödinger. In this role he oversees the research and execution of machine learning applications for Schrödinger’s digital chemistry platform. In 2017 he was a visiting researcher at the Pande Lab working on using deep learning techniques for drug discovery. During that time he co-authored MoleculeNet, a benchmarking paper analyzing machine learning techniques for chemoinformatics. Karl received his undergraduate degree from the University of Virginia, and a Master’s in machine learning from Georgia Tech.

AAPS 2024 PharmSci 360

Conference

AAPS 2024 PharmSci 360

CalendarDate & Time
  • October 20th-23rd, 2024
LocationLocation
  • Salt Lake City, Utah

Schrödinger is excited to be participating in the AAPS 2024 PharmSci 360 conference taking place on October 20th – 23rd in Salt Lake City, Utah. Join us for presentations by Schrödinger scientists. Stop by booth #2503 to speak with us.

icon time OCT 21 | 10:00AM – 10:30AM
icon location 251 F Salt Palace Convention Center
Coarse-Grained Modeling of Nucleic Acid-Loaded Lipid Nanoparticle Formulations

Speaker:
Doug Grzetic, Senior Scientist I, Schrödinger

Abstract:
We will start off with a problem statement describing how the complicated nature of lipid nanoparticle formulations makes efficient formulation optimization a challenge. Additionally, the effectiveness of LNP formulations is believed to be strongly correlated to the LNP morphology, but this is difficult to characterize, making predictive, in silico measurements extremely valuable. Then we will provide a brief description of molecular modeling, emphasizing that for LNP self-assembly length-scales (~100 nm) coarse-grained modeling is required. In addition, high-throughput screening studies require that the building of CG models be automated as much as possible. We briefly review techniques for the automation of this process. We demonstrate the application of coarse-grained modeling to RNA-encapsulating LNPs, with a case study focusing on the Pfizer-BioNTech COVID-19 vaccine formulation.

icon time OCT 21 | 3:15PM – 3:30PM
icon location 255 EF Salt Palace Convention Center
Modernize your arsenal of formulation tools with physics-based molecular simulation

Speaker:
Ben Coscia, Principal Scientist I, Schrödinger

Abstract:
The impact of physics-based molecular modeling and simulation on formulation is expanding rapidly with advancement of computer hardware and software algorithms. Cloud-based solutions enable individuals to access the world’s most powerful processors with just an internet connection. Machine learning algorithms continue to be leveraged towards improving the accuracy of our models and to guide high throughput simulation studies towards targeted properties. Despite this progress, one can argue that physics-based simulation is an underutilized technique, in large part due to slow adoption by non-experts. The purpose of this talk is to inform our audience of the accessibility of simulation and empower them to take the first steps towards interrogating their research questions with simulation, with specific emphasis on solubilization. We do this by example, describing two case studies which apply physics-based molecular simulation to gain insight into two different approaches that have direct implications on solubilizing poorly soluble APIs.

2024 AIChE Annual Meeting

Conference

2024 AIChE Annual Meeting

CalendarDate & Time
  • October 27th-31st, 2024
LocationLocation
  • San Diego, California

Schrödinger is excited to be participating in the 2024 AIChE Annual Meeting taking place on October 27th – 31st in San Diego, California. Join us for presentations by Schrödinger scientists. Stop by booth #521 to speak with us.

icon time OCT 28 | 8:00AM – 8:30AM
icon location Hilton San Diego Bayfront Hotel, Sapphire Ballroom E
Accelerating Polymer Design with Targeted Properties Using Machine Learning and Physics-Based Models

Speaker:
Alex Chew, Principal Scientist I, Schrödinger

Abstract:
Designing new, industrially relevant polymers is challenging because of the need to optimize multiple materials’ properties simultaneously, which is expensive and often infeasible using traditional trial-and-error approaches. One possible solution to identifying promising polymeric materials is to employ a combination of machine learning and physics-based tools to screen the polymer design space and provide suggestions for new polymers that meet the criteria for an industrial application. In this work, we demonstrate a workflow that utilizes machine learning and molecular modeling approaches to design new polymers (specifically, polycarbonates) that satisfy five polymer properties, including the glass transition temperature, optical properties, and mechanical properties. Using a relatively modest dataset of fewer than 200 points, we developed quantitative structure-property relationship (QSPR) models to accurately predict the experimental polymer properties given the homo- or co-polymer structures and composition as input. Leveraging these computationally efficient QSPR models, we then screened over ~10,000 polymer structures that were generated through R-group enumeration tools. We used these QSPR predictions to create multi-parameter optimization scores to help down-select the large polymer space to ~10 promising candidates. We validated the predicted properties of the top polymer candidates using classical molecular dynamics simulations and density functional theory, which revealed reliable correlation between physics-based and QSPR approaches. Finally, we validated the computational predictions against experiments, which showed good agreement with QSPR and physics-based models. Our workflow demonstrates the usefulness of combining data-driven and physics-based approaches in designing new polymers given a small dataset, which is broadly useful for scientists interested in leveraging computer-aided strategies to innovate new materials while mitigating the need for extensive trial-and-error experimentation.

icon time OCT 29 | 4:00PM – 4:30PM
icon location Hilton San Diego Bayfront Hotel, Aqua 300 (AB)
Capturing the unmeasurable: How atomistic simulations are bringing understanding to interfacial phenomena

Speaker:
Andrea Browning, Director, Schrödinger

Abstract:
Most materials development at some point must consider an interface. Between adhesives and component parts, between matrix and filler in composite materials, and between atomic layers during assembly, the interface impacts the overall performance of the product. But these surfaces can be difficult to probe experimentally. Atomistic level modeling and simulation techniques such as quantum mechanics and molecular dynamics allows a window into the specific interactions that accumulate into the observed interfacial behavior. As simulation techniques and compute power has grown, we are now better able to explore how interfaces behave. However, there are still challenges remaining such as accounting for reactions at complex, multicomponent interfaces. From battery solid electrolyte interphases to dissolving polymers at tablet interfaces, simulations must capture discrete interactions that are important to the interface in order to be useful. This talk will review examples from various industries in how simulation of interfaces has developed and the role of technology exploration in Dr. Browning’s career evolution.

Computational Medicinal Chemistry School

Conference

Computational Medicinal Chemistry School

CalendarDate & Time
  • October 28th-30th, 2024
LocationLocation
  • Cambridge, Massachusetts

Schrödinger is excited to be a Founding Sponsor at the Computational Medicinal Chemistry School conference taking place on October 28th – 30th in Cambridge, Massachusetts. Join us for a presentation by Andreas Verras, Director at Schrödinger, titled “Beyond Potency: How Modeling can contribute to ADMET with structure based, ligand property, and machine learning approaches.”

icon time OCT 28 | 2:15 – 3:00 PM
Beyond Potency: How Modeling can contribute to ADMET with structure based, ligand property, and machine learning approaches.

Speaker:
Andreas Verras, Director, Schrödinger

Abstract:
Potency optimization is a general first step in drug discovery, but can be quickly overshadowed by other problems that make in vivo studies impossible. Optimizing absorption, metabolism, efflux and off-target toxicities is necessary to generate molecules that can interrogate your mechanism in an animal and ultimately go to the clinic. I will explore modeling approaches to understanding pharmacokinetic data; improving efflux, absorption, and eflux; and modeling some off target data. A combination of structure based, ligand based, and machine learning approaches is presented with some opinion on which problems they are most suited.