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CUP XXIII - Santa Fe March 5-7, 2024

CUP XXIII - Santa Fe March 5-7, 2024

CUP is OpenEye's annual scientific meeting held at La Fonda on the Plaza in Santa Fe where we bring together top Scientists, Customers, Users, and Programmers in the industry to discuss the challenges in drug discovery. This year, in addition to a day of reports from OpenEye scientists, we will have two keynote speakers and four half-day sessions planned on the topics below.


Tuesday - March 5th, 2024 - Lumpkins Ballroom

8:00  - Registration opens - Breakfast buffet on the Mezzanine
9:00  - Introduction – Anthony Nicholls, OpenEye
9:30  - State of the Cloud – Jharrod LaFon, OpenEye 
10:00 - DMTA the Orion Way – Paul Hawkins & David Hamilton, OpenEye

10:30 - Break

11:00 - Science at OpenEye – Geoff Skillman, OpenEye 
11:20 - Overview of Applications and Toolkits – Matt Geballe, OpenEye
11:40 - 3D QSAR for Binding Affinity Prediction – Jingyi Chen, OpenEye

12:00 - Lunch Break (on own)

2:00 - Progress in Affinity Prediction on Orion – Chris Neale, OpenEye
2:30 - Macromolecular Refinement Using a Weighted Ensemble Sampling Approach – Steve Muchmore, OpenEye
3:00 - Advancements in Crystal Structure Prediction on Orion – Hari Muddana, OpenEye

3:30 - Break

4:00 - Solving the World’s Problems, One Cryptic Pocket at a Time Neha Vithani, OpenEye
4:30 - 3D Antibody Modeling in Orion Jesper Sørensen, OpenEye

5:00 - Break

5:15 - Frank K. Brown Industry Perspective Talk: Christian Cortis, COO of Tectonic Therapeutics:

"Connecting the Threads of Computation and Informatics over Decades in Biotech – Perspectives from Personal Experience"

6:00 - End of Session and Reception - La Terraza Banquet Room


Wednesday - March 6th, 2024 - Lumpkins Ballroom

8:00 - Registration opens – Breakfast buffet on the Mezzanine

Morning Session: Cheating at a very large scale
As virtual databases get larger and larger, how do we search such 3D chemical spaces efficiently?

9:00 - Comparing Massively-multitask Modeling Methods - Eric Martin, Novartis
9:30 - Shape Aware Synthon Search (SASS) for Virtual Screening of Synthon-based Chemical Spaces - Chen Cheng, Genentech

10:00 - Break

10:30 - AI Accelerated Multi Billion Scale Docking - Mark McGann, OpenEye
11:00 - Thompson Sampling – An Efficient Method for Searching Ultralarge Synthesis on Demand Databases - Pat Walters, Relay Therapeutics

12:00 - Lunch Break (on own)

Afternoon Session: Hype vs. Hope
Is the excitement around new techniques and technologies justified? Tell us of your experiences with LLMs, quantum computing, large-scale dynamics or any thing else that either lives up to its hype or doesn’t.

2:00 - Intro: Handling Hype (and Hope) Matt Geballe, OpenEye
2:15 - Check Out the Big Brain on Brad! - Kim Branson, GSK
2:45 - NVIDIA BioNeMo – Scaling the Training and Inference of Biomolecular LLMs – Greg Zynda, NVIDIA

3:15 - Break

3:45 - Leveraging Generative Modeling and Synthetic Biology to Design Next Generation Antibody Therapeutics - Hunter Elliott, BigHat
4:15 - Iambic NeuralPLexer: Protein-ligand Complex Structure Prediction with a Multi-scale Deep Generative Model Matt Welborn, Iambic

4:45 - Break

5:00 - Cyrus Levinthal Lecture: Charlotte Deane, Oxford University and the Executive Chair at the Engineering & Physical Sciences Research Council:

"Harnessing AI to Advance Biotherapeutics: From Structure to Affinity Prediction"
Antibodies are cornerstone immune system players, vital for vaccine responses and emerging as powerful biotherapeutics. However, traditional development can be lengthy and expensive, exceeding $1 billion. This talk explores how cutting-edge computational methods, particularly machine learning, hold immense promise for revolutionising biotherapeutics development. I will showcase our pioneering tools ranging from rapid, accurate structure prediction to binding affinity forecasting, highlighting both their potential and current limitations.

6:00 - Poster Session with Buffet Dinner - New Mexico and Santa Fe Ballrooms


Thursday - March 7th, 2024 - Lumpkins Ballroom

8:00 - Registration opens – Breakfast buffet on the Mezzanine

Morning Session: Structural Toxicology
As techniques such as cryoEM remove previous limits on what can be resolved, how much of ADME can we begin to model?

9:00 - Integrating Cryo-EM into Structural Toxicology: Addressing Off-target Effects & Optimizing Drug Development - Claudio Catalano, Nanoimaging
9:30 - CYP Conformational Properties from Molecular Dynamics Simulations & Implications for Structure-based CYP Toxicity Modeling - Olgun Guvench, University of New England

10:00 - Break

10:30 - Harnessing AlphaFold to Reveal State Secrets: Predictions of hERG Closed & Inactivated States - Khoa Ngo, UC Davis
11:15 - The “State of the Art” in Permeability Predictions: This is What Happens When Ant Tells You to Get Angry - David LeBard, OpenEye

12:00 - Lunch Break (on own)

Afternoon Session: Affinity
Although free-energy methods have made a significant impact, they aren’t as robust or accurate as we’d like.

2:00 - Water in Binding Free Energy Calculations - David Mobley, UC Irvine
2:30 - Free Energy Methods ain’t Free: The Methods in the Madness - Yutong Zhao, Relay Therapeutics

3:00 - Break

3:30 - Merging Experiments with Computations: Assessing Drug Fragments Using Free-energy Methods - Mark Ams, NM Tech
4:00 - Potency isn’t Everything: Glucokinase as a Drug Target for Type 2 Diabetes  - Kim Sharp, University of Pennsylvania
4:30 - ML/MM REPEX/ATM FEP/MBAR RBFEs and You – John Chodera, Memorial Sloan Kettering Cancer Center
5:00 - Closing Remarks - Anthony Nicholls, OpenEye

6:00 - Conference Dinner at Casa España

Penny J. Gilmer Memorial Grant:

To encourage scientists starting out in the computational chemistry field, OpenEye awards several travel grants to CUP. These grants are available to graduate students and post-docs of underrepresented genders in computational chemistry who intend to present their research at CUP. Apply here.

Hotel Reservations:
Discounted Hotel Rates at La Fonda can be found here.