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D3R 2018 Workshop Group Photo

Overview

Dates: Feb 22-23, 2018
Agenda
Hotel Block: La Jolla Shores Hotel
Online Registration: http://www.regonline.com/d3r2018 Last day to register is Feb 13.
Note: The registration fee includes breakfast, lunch, and dinner on Thursday and breakfast and lunch on Friday.

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!

La Jolla Shores Hotel

8110 Camino Del Oro, La Jolla, CA 92037
(855) 923-8058

Get Directions

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.
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