CUP XXI - Santa Fe | March 8-10, 2022

CUP XXI was held March 8-10, 2022 at La Fonda on the Plaza in Santa Fe, NM.

CUP is OpenEye's annual scientific meeting held in Santa Fe where we bring together top Scientists, Customers, Users, and Programmers in the industry to discuss the challenges in drug discovery.

Select presentations from CUP XXI are now available at the links below. Please check back often . We will be posting additional presentions as they become available.

Agenda

CUP Day 1 | Tuesday, March 8, 2022

OpenEye Day

Morning Session: Orion Present & Future – Jharrod LaFon

9:00 – Introduction – Anthony Nicholls, CEO

What's New in Orion (part 1)

9:30 – Advances in Orion High-Performance Computing – Andrew Shewmaker
9:50 – The Orion User Interface one year later – Joe Moon
10:10 – Break

What's New in Orion (part 2)

10:40 – Quantum Mechanics in Orion: It's not just for CSP anymore! – Caitlin Bannan
11:00 – Orion User Success: Videos, tutorials & development help – Brenda Montalvo
11:20 – The Orion Roadmap – Ash Jogalekar
12:00 – Lunch break

Afternoon Session: OpenEye Science – Geoff Skillman

2:00 – Gigadock Warp: Making docking billions of molecules accessible to everyone – Mark McGann
2:30 – Preparing MD-ready receptors for all therapeutic protein targets and beyond – Jesper Sørensen
3:00 – CSP is difficult, but not impossible! – Hari Muddana
3:30 – Break
4:00 – AbXtract: Rapidly generate antibody leads from next generation sequencing data – Frank Erasmus, Specifica
4:30 – Simulating passive membrane permeability with WESTPA – David LeBard
5:00 – Break
5:30 – Frank K. Brown Industry Perspective Talk: Eric Manas, SVP, Medicine Design, Treeline Biosciences

CUP Day 2 | Wednesday, March 9, 2022

Morning Session: General – Anthony Nicholls

9:00 – How We Built a Large-Scale Matched Pair Analysis Engine (MCPairs) using OpenEye Toolkits – Al Dossetter, MedChemica
9:30 – Adventures with Huge Chemical Spaces – Mark Seierstad, Janssen/Johnson & Johnson
10:00 – Exploring a Hypothetical Gigalibrary for Novel Structures and Functions – Ishika Saha, UCLA
10:30 – Break
11:00 – Molecular Dynamics Simulation Workflows for Macromolecular Crystallography – David Wych, Los Alamos Labs
11:30 – 10 Years at OpenEye came in handy after all – Brian Cole, Senior Director of Scientific Software, Treeline Biosciences
12:00 – Lunch break

Afternoon Session: CryoEM – Steve Muchmore

2:00 – CryoDRGN: Neural reconstruction of dynamic protein structures from Cryo-EM data – Ellen Zhong, Massachusetts Institute of Technology
2:30 – Phenix Tools for CryoEM – Christopher Schlicksup, Phenix Consortium
3:00 – Break
3:30 – Squeezing Blood from a Stone: Challenges in Single Particle CryoEM Data Processing – Phil McGilvray, NanoImaging Services
4:00 – Architecture of the erythrocyte ankyrin complex – Oliver Clarke, Columbia University Medical Center
4:30 – Break
5:00 – Levinthal Lecture: Giovanna Scapin, Chief Scientist, NanoImaging Services
6:00 – Poster Session & Buffet Dinner – Santa Fe & New Mexico Ballrooms, La Fonda Hotel

CUP Day 3 | Thursday, March 10, 2022

Morning Session: Protein-ligand binding free energies – Christopher Bayly

9:00 – High throughput relative and absolute non-equilibrium binding free energies with pmx – Bert de Groot, Max Planck Institute for Biophysical Chemistry
9:30 – Separated Topologies: Unchained from similarity – Hannah Baumann,
University of California – Irvine
10:00 – A Moonshot on theory and practice – John Chodera, Memorial Sloane Kettering Cancer Center
10:30 – Break
11:00 – Getting an edge with Non-Equilibrium Switching – Christopher Bayly, OpenEye
11:30 – Pursuing perfection by preventing pesky pathologies – David Mobley, University of California - Irvine
12:00 – Lunch break

Afternoon Session: Enhanced Sampling Molecular Dynamics – David LeBard

2:00 – Revisiting a textbook chemical reaction: Complete pathways and kinetics from hybrid QM/MM simulations – Lillian Chong, University of Pittsburgh
2:30 – Investigating the opening mechanism of the spike protein of SARS-CoV-2
– Shirley Ahn, McCammon Lab, University of California - San Diego
3:00 – Harnessing trajectory ensembles for rates, reaction coordinates, and mechanism – Jeremy Copperman, Zuckerman Lab, Oregon Health & Science University

3:30 – Break
4:00 – Sampling rare events: folding pathways of proteins G and L – Alberto Perez, University of Florida
4:30 – DeepDriveMD: AI-accelerated enhanced sampling for molecular dynamics simulation – Heng Ma, Ramanathan Lab, Argonne National Laboratory
5:00 – Closing Remarks - Anthony Nicholls
6:00 – Closing Night Dinner – Lumpkins Ballroom, La Fonda Hotel