ONLINE: Molecular Modeling with Schrödinger-Suite Workshop

The Schrödinger drug discovery platform encompasses solutions for predictive physics-based modeling, machine learning, data analytics, and collaboration. Through hands-on exercises and interactive presentations, we will work together with the attendees on industrial-level computational modelling tasks in the fields of chemical & biological molecular design. Beginning from target analysis and preparation of compound library via enumeration and virtual screening cascades involving ligand- and structure-based methodologies. 

During this workshop, we will give an overview and hands-on training on the Schrödinger Materials Science Suite. We will particularly focus on efficient structure generation, automated workflows and property-oriented analysis tools, which are important to overcome challenges towards wider application of computational tools in the rational design of new materials in industry. We will discuss simulation approaches for different length and time scales, including quantum mechanics and molecular dynamics, as well as machine learning. The application areas and the level of complexity of the hands-on sessions will be tailored to the interests of the participants as stated in the registration form. Examples for possible focus areas could be, among others, polymers and soft matter, molecular reactivity and catalysis, organic electronics, solid-state materials, or machine learning. The final agenda and hands-on sessions will be announced closer to the event.   

The final agenda and hands-on sessions (on Schrodinger Cluster) will be announced closer to the event.

A tentative agenda: 

Each workshop is organized into two sessions with parallel tracks and a one-hour lunch break.

Wednesday, December 02, 2020

09:00 - 12:00  Drug Discovery with Schrödinger Suite (Part 1)
 During this day, you will get introduced to the following Schrödinger tools and workflows: 

• Target analysis and preparation: Protein Preparation Wizard, Sitemap, Watermap, and Molecular Dynamics using Desmond GPU

• Compound enumeration to generate a synthetically feasible library as the starting point for a virtual screening: Pathfinder, Reaction-based Enumeration, LigPrep

• Compound evaluation/Virtual screening using a combination of ligand- and structure-based approaches: Shape GPU, Glide, FEP+

12:00 - 13:00 Lunch Break

13:00 - 14:00 Schrödinger Suite-Biologics (Antibody modeling, Residue scanning, Peptide modeling) 

14:00 - 15:00 PyMOL (Dr. David Wifling) 

Thursday, December 03, 2020

10:00 - 12:00 Polymer Developement and Discovery with Computational Materials Simulations  (Part 1)
 First, we will consider principles of automation of three main steps in computational modelling:

• Atomic structure generation;

• Properties calculations;

• Calculation analysis.     

12:00 - 13:00 Lunch Break 

13:00 - 15:00 Polymer Developement and Discovery with Computational Materials Simulations  (Part 2)

Photos: Participants of the Schrodinger Workshop 2017

The event is provided free of charge for the participants.

After this workshop, participants ... 

• ... will have a detailed understanding of the essential MD with Schrodinger simulations

• ... will have gained knowledge about Molecular Visualization ...

Schrödinger software experts 

Registration via Schrödinger: https://docs.google.com/forms/d/e/1FAIpQLSfLvyxBfdoUt1QOoscQ0DvgP4AcxiRfe63KzFC7BNqHZ4eHvw/viewform.   

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