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Overview
Dates: Feb 22-23, 2018
Agenda
Wednesday, February 21 at La Jolla Shores Hotel
| 6 - 8 PM | Reception |
Thursday, February 22 at Scripps Institute of Oceanography Forum (SIO)
| 7:30 AM | Shuttle from La Jolla Shores Hotel to SIO |
| 7:45 AM | Shuttle from La Jolla Shores Hotel to SIO |
| 8:15 AM | Breakfast on-site |
| Welcome and Updates | |
| 9:00 - 9:30 AM | Welcome and D3R Update — Mike Gilson and Rommie Amaro, D3R, UC San Diego |
| 9:30 - 9:40 AM | NIH Perspective — Peter Lyster, NIGMS, NIH |
| Grand Challenge 3 Reports | |
| 9:40 - 10:15 AM | Evaluation Overview of GC3 — Mill Lambert & Neysa Nevins, GSK |
| 10:15 - 10:30 AM | Break |
| 10:30 - 10:50 AM | GC3 Participant Talk 1 — Maxim Totrov, MolSoft |
| 10:50 - 11:10 AM | GC3 Participant Talk 2 — Guo-wei Wei, Michigan State |
| 11:10 - 11:30 AM | GC3 Participant Talk 3 — David Koes, University of Pittsburgh |
| 11:30 - 11:50 AM | GC3 Participant Talk 4 — Ashutosh Kumar, RIKEN |
| 11:50 - 12:10 PM | Open Discussion on Evaluation Metrics — D3R Moderator |
| 12:10 - 1:30 PM | Lunch at SIO |
| SAMPL6 Reports | |
| 1:30 - 1:40 PM | SAMPL6 Intro — John Chodera, MSKCC |
| 1:40 - 1:55 PM | SAMPL6 host-guest intro and overview — Andrea Rizzi, MSKCC |
| 2:00 - 2:15 PM | SAMPL6 host-guest participant 1 — Michail Papadourakis, Edinburgh (video presentation) |
| 2:15 - 2:30 PM | SAMPL6 host-guest participant 2 — Marie Laury, Washington University |
| 2:30 - 2:50 PM | SAMPLing challenge overview and results — Andrea Rizzi, MSKCC |
| 2:50 - 3:05PM | Break |
| 3:05 - 3:25 PM | SAMPL6 pKa intro and overview — Mehtap Isik, MSKCC |
| 3:25 - 3:40 PM | SAMPL6 participant 1 — Samarjeet Prasad |
| 3:40 - 3:55 PM | SAMPL6 participant 2 — Qiao Zeng, NIH |
| 3:55 - 4:10 PM | SAMPL6 participant 3 —Marvin Waldman, Simulations Plus |
| 4:15 - 6:00 PM | Poster Session, Sunset (5:30PM) with Snacks and Liquid Refreshments |
| 6:00 - 7:30 PM | Dinner on the patio at SIO |
| 7:30 PM | Walk or Ride Share Back to La Jolla Shores Hotel |
| 8:05 PM | Shuttle from SIO Forum to La Jolla Shores Hotel |
| 8:15 PM | Shuttle from SIO Forum to La Jolla Shores Hotel |
Friday, February 23 at Scripps Institute of Oceanography Forum (SIO)
| 7:30 AM | Shuttle from La Jolla Shores Hotel to SIO |
| 7:45 AM | Shuttle from La Jolla Shores Hotel to SIO |
| 8:15 AM | Breakfast on-site |
| Perspectives and Lessons Learned from D3R and SAMPL | |
| 9:00 - 9:10 AM | Introduction to Day 2 — Mike Gilson and Rommie Amaro |
| 9:10 - 9:40 AM | A Longitudinal View of the Grand Challenges — Pat Walters, Relay Therapeutics |
| 9:40 - 10:00 AM | A Longitudinal View of the SAMPL Challenges — David Mobley, UC Irvine |
| 10:00 - 10:20 AM | D3R Lessons Learned — Alexandre Bonvin, Utrecht U (Video Conference) |
| 10:20 - 10:40 AM | SAMPL Lessons Learned — Bogdan Iorga, ICSN, CNRS |
| 10:40 - 11:00 AM | Break |
| Workflows for CADD and Evaluation of CADD Methods | |
| 11:00 - 11:20 AM | Continuous Evaluation of Ligand-Protein Predictions (CELPP) — Jeff Wagner, D3R, UC San Diego |
| 11:20 - 11:40 AM | GC and CELPP: Workflows and Insights —Xiaoqin Zou, U. Missouri |
| 11:40 - 12:00 PM | MoISSI and Workflows — John Chodera, Memorial Sloan Kettering |
| 12:00 - 12:30 PM | Open Discussion on Enabling Adoption of Workflows |
| 12:30 - 1:30 PM | Lunch at SIO |
| 1:30 - 1:45 PM | Group photo |
| Future Directions | |
| 1:45 - 2:00 PM | Upcoming D3R and SAMPL Challenges — Mike Gilson, Rommie Amaro, David Mobley |
| 2:00 - 3:15 PM | D3R Community Feedback Discussion Datasets—Attributes, Types, Size, Number/Challenge Challenges and Workshops—Timing, Type, Frequency Challenge Evaluations—Website Posting Future funding / support of blinded prediction challenges |
| 3:15 - 3:30 PM | Wrap-up and Conclusions — Mike Gilson and Rommie Amaro |
| 3:30 PM | Workshop concludes |
| 3:30 PM | Shuttle from SIO Forum to La Jolla Shores Hotel |
| 3:45 PM | Shuttle from SIO Forum to La Jolla Shores Hotel |
| 4:00 - 5:00 PM | SAB Meeting (closed session) |
| 5:00 - 5:30 PM | SAB Session with D3R PIs |
| 5:30 PM | Shuttle from SIO Forum to La Jolla Shores Hotel |
| 6:00 PM | SAB Dinner at La Jolla Shores Hotel |
2018 Workshop Presentations
Welcome and Updates
Mike Gilson and Rommie Amaro, D3R, UC San Diego
Welcome and D3R Update 
Peter Lyster, NIGMS, NIH
NIH Perspective
Grand Challenge 3 Reports
Mill Lambert & Neysa Nevins, GSK
Evaluation Overview of GC3
Maxim Totrov, MolSoft
Pose and affinity prediction by ICM in D3R GC3
Guo-wei Wei, Michigan State
Integrating Mathematics and Machine Learning for Drug Design
David Koes, University of Pittsburgh
Protein-Ligand Scoring with Convolutional Neural Networks
Ashutosh Kumar, RIKEN
A Pose Prediction Approach based on Ligand 3D Shape Similarity: Lessons learned in D3R challenge
Open Discussion on Evaluation Metrics
SAMPL6 Reports
David Mobley, UC Irvine
SAMPL6 Overview
Andrea Rizzi, MSKCC
Overview of the SAMPL6 host- guest challenge
Michail Papadourakis, Edinburgh
SOMD- lessons learned from SAMPL6
Marie Laury, Washington University
The SAMPL6 Host-Guest Challenge with the AMOEBA force field
Andrea Rizzi, MSKCC
SAMPLing challenge overview and results
Mehtap Isik, MSKCC
SAMPL6 pKa intro and overview
Samarjeet Prasad, JHU/NIH
A hybrid QM and MM approach for pKa prediction
Qiao Zeng, NIH
QM-based pKa prediction using absolute scheme
Marvin Waldman, Simulations Plus
SAMPL6 pKa Challenge: Predictions of ionization constants performed by the S+pKa method implemented in ADMET PredictorTM software
Perspectives and Lessons Learned from D3R and SAMPL
Pat Walters, Relay Therapeutics
A Longitudinal View of the Grand Challenges
David Mobley, UC Irvine
A Longitudinal View of the SAMPL Challenges
Alexandre Bonvin, Utrecht U
D3R Lessons Learned
Bogdan Iorga, ICSN, CNRS
pKa prediction on the SAMPL6 dataset — Lessons learned
Workflows for CADD and Evaluation of CADD Methods
Jeff Wagner, D3R, UC San Diego
Continuous Evaluation of Ligand-Protein Predictions (CELPP)
Xiaoqin Zou, U. Missouri
GC and CELPP: Workflows and Insights
John Chodera, Memorial Sloan Kettering
Reproducible Workflows: the way forward
Open Discussion on Enabling Adoption of Workflows
A wish list for CELPP
Future Directions
Upcoming D3R and SAMPL Challenges, Mike Gilson, Rommie Amaro, David Mobley
JCAMD Special Issues, Terry Stouch
D3R Community Feedback Discussion
Wrap-up and Conclusions, Mike Gilson and Rommie Amaro
Weather Advisory
We'll be experiencing uncommon "winter" weather during the workshop. The temperature will be in the 40s/50s with a possibility of rain!
Robert Paine Scripps Forum for Science, Society, and the Environment
8610 Kennel Way (formerly Discovery Way), La Jolla, CA 92037
Driving Directions
From Hwy 5
- Head west on La Jolla Village Drive towards Birch Aquarium.
- Turn left onto Expedition Way.
- Stop at the stop sign right before the Aquarium. Turn right on Downwind Way.
- This road curves to the left so follow it to the end.
- Turn left onto La Jolla Shores Drive.
- Turn right onto El Paseo Grande.
- Turn right into the parking lot... this is Kennel Way.
From Hwy 52
- Take 52 West, La Jolla Parkway.
- La Jolla Parkway continues down a hill into La Jolla and turn right onto La Jolla Shores Drive.
- Turn left onto El Paseo Grande.
- Turn right into the parking lot... this is Kennel Way.
About
Welcome to the Drug Design Data Resource Community. D3R is funded in part by NIH grant 1U01GM111528 from the National Institute of General Medical Sciences
