MAR 26, 2025
Accelerating protein degrader discovery: Computational strategies for degrader design and optimization
Protein degraders have emerged as a promising modality in drug discovery, offering a novel mechanism for modulating protein function by leveraging the cell’s natural degradation pathways. However, designing protein degraders presents unique challenges due to their bifunctional nature, requiring complex optimization across multiple parameters.
Schrödinger has engaged in collaborative research projects with industry scientists to develop computational workflows that can accurately predict the structure of ternary complexes between two protein partners and a bifunctional molecule. In this webinar, we will showcase Schrödinger’s advanced computational toolkit, which integrates protein-protein docking and linker sampling to generate an ensemble of possible complexes, metadynamics to accurately score these complexes, and free energy perturbation (FEP+) calculations to optimize degrader potency.
Join us to explore how these workflows can accelerate the design of protein degraders—from predicting ternary complexes to optimizing linker properties—and can empower real-time collaboration through Schrödinger’s LiveDesign platform.
Webinar Highlights:
- Summary of current trends and challenges in the modeling of protein degraders
- Overview of Schrödinger computational solutions, including exit vector sampling, ternary complex ensemble prediction and filtering using experimental information like HDX-MS, ternary complex scoring, and linker optimization using FEP+
- Demo of workflows in LiveDesign to streamline the degrader design process
- Sneak peak of upcoming Maestro panels for protein degrader modeling
Our Speakers
Agus Rodriguez-Granillo
Director, Application Science, Schrödinger
Agus leads the Application Science team in Cambridge, MA, supporting customers in the Northeastern region of the U.S. In addition to customer support, Agus has a strong interest in bifunctional degraders as a new therapeutic modality and has been actively working in this area. Agus is originally from Argentina and earned her Ph.D. in Biochemistry at Rice University in Houston, TX.
Sonia Nicolaou
Senior Scientist II, Application Science, Schrödinger
Sonia Nicolaou is an All Access Application Scientist at Schrödinger based in Cambridge, MA. She received her PhD in Chemistry from the University of Manchester, UK. Since joining Schrödinger she has been providing scientific support to customers and has been involved in the development of new models in LiveDesign. Her more recent efforts have been focused on the implementation of PROTACs workflows in LiveDesign.
MAR 23 | 8:00AM 
Ballroom 20D 
