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CUP XVII - Santa Fe | Mar. 6 2017

CUP XVII - Santa Fe | Mar. 6 2017

This years CUP event was held from March 6-8, 2017 at the Inn and Spa at Loretto in Santa Fe, NM. 


Sunday, March 5, 2017

  • 7:00 - 10:00 pm - Reception - Penthouse Suite

Monday, March 6, 2017

Morning Session:

Afternoon Session:

  • 2:00 - Toolkit Update -  Krisztina Boda, Head of Toolkits, OpenEye
  • 2:20 - Product Update -  Mark McGann, Head of Scientific Applications, OpenEye
  • 2:40 - Macrocycle ConformationsPaul Hawkins, Head of Scientific Solutions, OpenEye
  • 3:00 - OpenEye Science in Orion:
    Protein Data as a Cloud Service - Bob Tolbert, CTO, OpenEye
    Molecular DynamicsChristopher Bayly, OpenEye, David Mobley, UCI
  • 4:00 - Tea Time
  • 4:30 - Frank K. Brown Address: Comp Chem. W(h)ither Thou? - Cathy Peishoff, ex-GSK

  • 7:00 - 10:00 pm  - Reception -  Penthouse Suite

Tuesday, March 7, 2017

Morning Session: Practical Quantum Mechanics

  • 9:00 -  A Robust and Accurate Tight-binding Method for Structures and Non-covalent Interaction Energies - Christoph Bannwarth, U. Bonn
  • 9:30 -  Applications of Quantum Chemistry in Molecular Design and Recognition - Daniel Cheney, BMS
  • 10:00 - Tea Time
  • 10:30 - Surfing Wave Functions in the Cloud - J.W. Feng, Denali Therapeutics
  • 11:00 - The Mysteries of Chirality and Optical Activity - T. Daniel Crawford, Virginia Tech
  • 11:30 -  Solubility & Binding - Tom DardenOpenEye
  • 12:00 - Lunch

Afternoon Session: Things I Wish Academics Would Pay More Attention To.

  • 2:00 - How Did We Get to be Such a Dysfunctional Field? - Anthony Nicholls, OpenEye
  • 2:30 - Tilting at Windmills – A Few Ideas Beyond Binding - Stephen Johnson, BMS
  • 3:00 - Rates and Routes of Metabolism - Dan McMaster, Vertex Pharmaceuticals
  • 3:30 - Reproducible Academic Research: From Frequentist and Bayesian Approaches in Hypothesis Testing to Blinded Preclinical Experimental Design -  Greg TawaNIH/NCATS
    4:00 - Tea Time
  • 4:30 - The Levinthal Lecture - John Conway, LabAnswer
  • 6:00 - 9:00 pm - Poster Session (see titles below), Demos of Orion and MMDS (Macromolecular Data Service)

Wednesday, March 8, 2017

Morning Session: Things I Wish Academics Would Pay More Attention To.
  • 9:00 -Is There Overlooked Gold in Our HTS Data or “Could a Couple More Hours of Early Analysis Have Saved Your Project?” - Carleton Sage, Beacon Discovery
  • 9:30 - Does Quantity Beat Quality and Why Don’t We Know? - Anthony Nicholls, OpenEye
  • 10:00 - Tea Time
  • 10:30 - What’s Wrong with Trying to Predict Affinity, Anyway? - Eric Manas, GSK
  • 11:00 - An Academic Reposte -  Tudor Oprea, UNM
  • 11:30 - Roundtable
  • 12:00 - Lunch

Afternoon Session: Protein Modeling
  • 2:00 - Developing Cyrus Bench – Rosetta with Graphic Interface, Cloud Computing and Automated Workflows - Yifan Song, Cyrus Bioscience
  • 2:30 - From Gene to Structure: Enabling Structure Based Drug Discovery - Jesper SoerensenDart Neuroscience
  • 3:00 - Validating Water Placement: Experimental and Computational Methods - Greg Warren, Mike Word, OpenEye & Mike Wall, LANL
  • 3:30 - Tea Time
  • 4:00 - What Happened When Ant Let Us Put MD on Orion: Fragment Binding Occupancies Using BLUESDave MobleyUCI
  • 4:30 -  Can Free Energies Really Be Free? Alchemical Free Energy Calculations in the Cloud - John Chodera, Sloan-Kettering
  • 5:00 - Meeting Close
  • 6:00 - Conference Dinner - Rio Chama Steakhouse  414 Old Santa Fe Trail, (505) 955-0765

Poster Session:

CUP Guests

  • Yusuf Adeshina - University of Kansas - Using Small-molecules to Probe RNA-Protein Interactions
  • Caitlin C. BannanUniversity of California, Irvine - Improving Force Field Parameterization with Bayesian Inference for Chemical Perception
  • Tudor Oprea -University of New Mexico  – Unexplored Opportunities in the Human Druggable Genome
  • Michael Shirts - University of Colorado – What is the Effect of Including Entropic Effects in Predictions of Crystal Polymorph Stability?
  • Terry Stouch - Science for Solutions, LLCIs Your Work Significant? (Statistically That is!)
  • Matt Wessel - Patheon - Thermodynamic Behavior of Amorphous Solid Dispersions Predicted by Molecular Dynamics


  • Krisztina Boda - Faster 2D Fingerprint Comparison” & “Protein-Ligand 2D Depiction
  • Craig Bruce & Jeff Grandy - The Four Scenarios for Orion + a Potential Free Option
  • Jeff FlinnVida, Present & Future
  • Laszlo Fusti-Molnar & Anthony Nicholls - Multipolar ZAP for EON and Solvation
  • Burt Leland - HTS Assessment Using Maximum Common Substructure Tanimoto
  • Mark McGann & Grigory Ovanesyan - Kriging and PLS: Getting the Best of Both Worlds?
  • Joe Moon & Kevin Schmidt -A Roadmap for a UI Toolkit in Orion
  • Steve Muchmore - NIH Data for Virtual Screening Assessment
  • Shyamal Nath - A Toolkit for FreeForm
  • Perri Needham - Advances in FastROCS
  • Grigory Ovanesyan - Special Function Representations of Ligand and Protein Shapes
  • Mike Word and Greg Warren – Building Hydrogen Bonding Networks



Hotel Reservations
The meeting will take place at the Inn and Spa at Loretto in Santa Fe, NM. We have a block of rooms reserved there at a special rate of $141 per night. Reserve your room now to ensure you get the conference rate. You may also call the hotel directly to make reservations. The group code for phone in reservations is 10K83G and also may be referred to by your group name OpenEye Scientific SoftwareIndividual guests may call Reservations Toll Free at 866-582-1646 to reserve a room.

Fly into either Albuquerque International Sunport or Santa Fe Municipal Airport.

From Albuquerque International Sunport: Car rentals are available at the airport. The Sandia Shuttle Express leaves directly from the airport and makes several stops in downtown Santa Fe.

From Santa Fe Municipal Airport: Car rentals from Enterprise Rent-a-Car and Budget are available at the airport. Roadrunner Shuttle to downtown Santa Fe is also available within the airport. Please note: there are no taxi companies with locations at the airport. Capital City Cab is available for trips to and from the airport but transportation must be arranged with them by calling (505) 438-0000.

Second Annual “Penny J. Gilmer Grants” for Women Graduate Students and Post-docs

To encourage women starting out in our field, OpenEye is awarding several travel grants (reimbursements for transport and hotel) to female graduate students or post-docs in the US or Canada wishing to attend CUP and present posters or talks.

These grants are named for Penny J. Gilmer, PhD, now the Nancy Marcus Professor Emerita of Chemistry and Biochemistry at Florida State University. Penny, our CEO’s original academic mentor, was the first woman hired as tenure-track faculty at FSU’s Chemistry Department. She has been recognized by several organizations for her work as both a scientist and advocate, including the National Science Foundation, the American Association for the Advancement of Sciences, and the American Association of University Women. In 2008, she was chosen as a Fellow of the Association for Women In Science for her dedication to supporting women in science and engineering.

To apply, please contact Beatrice Montoya with your proposed topic. Awards will be finalized by the end of January.