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Computer Aided Drug Design (GRS)
Gordon Research Seminar

Predicting Pharmaceutically Relevant Endpoints: From Molecular Interactions to Holistic Approaches

Dates

July 15-16, 2017

Location

Mount Snow
West Dover, VT Site Information

Organizers

Chairs:
Julian E. Fuchs & Andrea Volkamer

Application Deadline

The application deadline for this meeting was June 17, 2017. You may still submit an application, which may be considered by the conference chair if there is still room available.

Meeting Description

Overview

The Gordon Research Seminar on Computer Aided Drug Design is a unique forum for graduate students, post-docs, and other scientists with comparable levels of experience and education to present and exchange new data and cutting edge ideas.

The aim of this GRS is to allow the participants to acquire a broader picture of the exciting new developments in the field and to identify new unmet needs. The format supports the participants to informally get to know the other people in the field who are at a similar scientific stage and provides a platform for discussion including directives for their career paths.

This GRS will focus on the latest developments in computer-aided drug design, covering a diverse range of methods from cheminformatics to molecular simulations. Data-driven as well as physics-based approaches are welcome focusing on individual molecular interactions as well as holistic tasks to predict pharmaceutically relevant endpoints, i.e. novel therapeutic targets and pockets, ligand binding, polypharmacology, or toxicity. Special attention will also be put on open source code and data bases or web services.

Instruction for applications: All talks slots are reserved for young scientists. All participants are expected to apply for a talk, with those not selected for giving a talk being expected to present a poster.

Application Instructions

The meeting will feature approximately 10 talks and 2 poster sessions. All attendees are expected to actively participate in the GRS either by giving an oral presentation or presenting a poster. Therefore, all applications must include an abstract.

The Chairs will select speakers from abstracts submitted by April 15, 2017. Those applicants who are not chosen for talks and those who apply after the deadline to be considered for an oral presentation will be expected to present a poster. In order to participate, you must submit an application by the date indicated in the Application Deadline section above.

Related Meeting

This GRS will be held in conjunction with the "Computer Aided Drug Design" Gordon Research Conference (GRC). Those interested in attending both meetings must submit an application for the GRC in addition to an application for the GRS. Refer to the associated GRC program page for more information.

Meeting Program

Saturday
2:00 pm - 5:00 pmArrival and Check-in
3:30 pm - 3:45 pmIntroductory Comments by GRC Site Staff / Welcome by the GRS Conference Chair
3:45 pm - 4:30 pmBottom-Up CADD: QM and Forcefields
Discussion Leader: Henrik Keranen (Janssen Research and Development, Belgium)
3:45 pm - 3:55 pmVladimiras Oleinikovas (University College London, United Kingdom)
"Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations"
3:55 pm - 4:00 pmDiscussion
4:00 pm - 4:10 pmMaciej Majewski (University of Barcelona, Spain)
"Extending the Quasi-Bound Concept to Multiple Interaction Points"
4:10 pm - 4:15 pmDiscussion
4:15 pm - 4:25 pmDaniel Mermelstein (University of California, San Diego, USA)
"Fast, Accurate pH Dependent Alchemical Free Energy Calculations Towards Rational Drug Design"
4:25 pm - 4:30 pmDiscussion
4:30 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmStructure-Based CADD: Molecular Interactions and Dynamics
Discussion Leader: Florent Chevillard (Kolb Lab, Philipps-Universität Marburg, Germany)
7:30 pm - 7:45 pmXavier Lucas (University of Dundee, United Kingdom)
"Mix 'n' Match: Towards Unbiased Computational Probing of Protein Surfaces"
7:45 pm - 7:50 pmDiscussion
7:50 pm - 8:05 pmJagna Witek (Swiss Federal Institute of Technology in Zurich (ETH Zurich), Switzerland)
"Kinetic Models of Cyclosporin A and E to Rationalize Their Membrane Permeability"
8:05 pm - 8:10 pmDiscussion
8:10 pm - 8:25 pmPrakash Chandra Rathi (Astex Pharmaceuticals, United Kingdom)
"Predicting 'Hot' and 'Warm' Spots on Proteins for Fragment Binding"
8:25 pm - 8:30 pmDiscussion
8:30 pm - 8:45 pmKai Sommer (University of Hamburg, Germany)
"Fragment Growing Linked with User Constraints Through Intuitive Usage"
8:45 pm - 8:50 pmDiscussion
8:50 pm - 9:05 pmMagdalena Korczynska (University of California, San Francisco, USA)
"Virtual Screening Identifies Selective Allosteric Modulator for the M2 Muscarinic Receptor"
9:05 pm - 9:10 pmDiscussion
9:10 pm - 9:25 pmRichard Lonsdale (AstraZeneca, United Kingdom)
"Predictive Computational Approaches to Enable Covalent Targeting of Cysteine Residues in Drug Discovery Projects"
9:25 pm - 9:30 pmDiscussion
Sunday
7:30 am - 8:30 amBreakfast
9:00 am - 11:00 amKnowledge-Based CADD: March of the Machines
Discussion Leader: Fiorella Ruggiu (Novartis Institutes for BioMedical Research, USA)
9:00 am - 9:15 amZied Gaieb (University of California, San Diego, USA)
"D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies"
9:15 am - 9:20 amDiscussion
9:20 am - 9:35 amBharath Ramsundar (Stanford University, USA)
"Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity"
9:35 am - 9:40 amDiscussion
9:40 am - 9:55 amDante Pertusi (Merck & Co., Inc., USA)
"Prospective Assessment of Virtual Screening Heuristics Derived Using a Novel Fusion Score"
9:55 am - 10:00 amDiscussion
10:00 am - 10:15 amPriyanka Banerjee (Charité - Universitätsmedizin Berlin, Germany)
"Computational Methods for the Prediction of Chemical Toxicity"
10:15 am - 10:20 amDiscussion
10:20 am - 10:35 amAmbrish Roy (Vertex Pharmaceuticals, USA)
"Harnessing the Power of Implicit Social Relationship Algorithms for Off-Target Activity Prediction"
10:35 am - 10:40 amDiscussion
10:40 am - 10:55 amNadine Schneider (Novartis Institutes for BioMedical Research, Switzerland)
"Chemical Topic Modeling: Exploring Molecule Datasets Using a Common Text-Mining Approach"
10:55 am - 11:00 amDiscussion
11:00 am - 12:30 pmPoster Session

Coffee will be served in the poster area from 11:00 am - 11:30 am
12:30 pmLunch
1:30 pm - 2:30 pmMentorship Component: CAMD: Career-Accelerating Mentoring Discussion
Discussion Leader: Aysegul Ozen (Genentech, Inc., USA)
1:30 pm - 2:30 pmPanel Discussion
"Mentorship Component: CAMD: Career-Accelerating Mentoring Discussion"
  • Paul Czodrowski (EMD Serono, Germany)
  • Matthias Rarey (University of Hamburg, Germany)
  • Patrick Walters (Relay Therapeutics, USA)
2:30 pm - 3:00 pmEvaluation Period
Fill in GRS Evaluation Forms
3:00 pmSeminar Concludes
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