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Conference Program
 
Computer Aided Drug Design
July 21-26, 2013
Mount Snow Resort
West Dover, VT
Chair:
Martin Stahl

Vice Chair:
Anthony Nicholls

The Gordon Research Conference on Computer-Aided Drug Design has been a premier conference in its field for more than three decades. During this period, there has been an ever-increasing interest in the application of computation to drug discovery, ranging from the all-atom simulation of molecular systems to the canonicalization and organization of molecular information. Some approaches, in particular molecular informatics, are now cornerstones of any drug discovery process. Statistics, data mining, machine learning and related concepts pervade today's drug discovery and development activities. An ever-important aspect of such research is the evaluation of progress: Is one method actually better than another? The program will be an unusual mix of cutting-edge, largely unpublished work in computational drug discovery, and lectures from experts outside the field who can give a broader view of the fundamental problems listed above and thus can illuminate the field’s greatest opportunities.

A four pronged approach is planned. (1) To canvas for presentations of techniques from which investigators might gain insight and which are less-well known than such value might imply. (2) To solicit work and presentations on major statistical issues in the field of CADD, namely the incorporation of error in both experimental data and computational process in the construction of models, methods to address over-parameterization of models, the assessment of the consequences of the non-ideality of retrospective datasets derived from the medicinal chemistry process, and the use and choice of appropriate NULL models in assessing new approaches. (3) To ask for allocutions from senior members of the field as to how statistical standards might be established and, finally, (4) presentations of perspectives from other disciplines. In addition, it is planned to have hands-on sessions where attendees may work with community data or bring their own and gain advice from experts. It is hoped that this conference will lead to regular self-assessment in the field of molecular modeling, standards for publication and presentations and help advance the rigorous discrimination of approaches to drug design and discovery.

The 2013 conference will for the second time take place in Mount Snow Resort, VT. It will bring together experts from industry and academia for the presentation of cutting-edge research and for open and stimulating thought exchange. As in the past, there will be ample time for discussion. Discussion sessions are lively and controversy is welcomed. All conferees are encouraged to present posters, wherein new science is presented along with statistical validation of the results. This meeting is typically oversubscribed, and we encourage submission of applications by early 2013. Participants will be a mix of researchers from industry, academia, and government, of different ages, backgrounds, and countries. Despite the popularity of the conference, this particular set of topics is especially pertinent to students, postdocs, and young investigators new to the field, who therefore should not hesitate to apply.


Contributors

SUNDAY
2:00 pm - 9:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:45 pmIntroductory Comments by GRC Site Staff / Welcome by the GRC Conference Chair
7:45 pm - 8:30 pmStatistics and Societal Issues, Part I
Discussion Leader: Glen Kellogg (VCU, Richmond, VA, USA)
7.45 pm - 8:15 pm Craig Bruce (OpenEye Scientific Software, Santa Fe, NM, USA)
"Pandora's Box Plot"
8:15 pm - 8:30 pm Discussion
8:30 pm - 9:30 pmExternal Perspectives, Part I
Discussion Leader: Anthony Nicholls (OpenEye Scientific Software, Santa Fe, NM, USA)
8:30 pm - 9:15 pm Stephen T. Ziliak (Trustee and Professor of Economics, Roosevelt University, Chicago, IL,USA)
"The Cult of Statistical Significance and the Future of Biometrics after Matrixx v. Siracusano"
9:15 pm - 9:30 pm Discussion
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 10:30 amPractical Statistics, Part I
Discussion Leader: Haihong Ni (BioDuro, Beijing, China)
9:00 am - 9:15 am Peter W. Kenny (Universidade de São Paulo, Brazil)
"Tales of Correlation Inflation: Eu prefiro a minha comida cozida e meus dados brutos"
9:15 am - 9:20 am Discussion
9:20 am - 9:35 am Maria A. Gallardo (Universidad de Zaragoza, Zaragoza, Spain)
"Outliers in Theory and Experiment: Lessons from Small Molecule Dipole Moments"
9:35 am - 9:40 am Discussion
9:40 am - 9:55 am Pat Walters (Vertex Pharmaceuticals, Boston, USA)
"Just Because You Published It Doesn't Make it Right"
9:55 am - 10:00 am Discussion
10:00 am - 10:30 am Group Photo / Coffee Break
10:30 am - 12:30 pmDeeper Issues for Statistics in CADD: Non-ideality
Discussion Leader: Martin Stahl (Roche, Basel, Switzerland)
10:30 am - 11:15 am Tom Darden (OpenEye Scientific Software, Santa Fe, NM, USA)
"Ideality is Overrated: Making the Most of an Imperfect World"
11:15 am - 11:30 am Discussion
11:30 am - 12:15 pm Anna Linusson (Umeå University, Umeå, Sweden)
"Cost and Correlation: Designing Better Data From the Start"
12:15 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 6:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 8:30 pmStatistics and Societal Issues, Part II
Discussion Leader: Yvonne Martin (AbbVie, Chicago, IL, USA)
7:30 pm - 8:15 pm Ajay Jain (UCSF, San Francisco, CA, USA)
"The Drunk and the Lamppost: Statistics may Support but not Illuminate"
8:15 pm - 8:30 pm Discussion
8:30 pm - 9:30 pmExternal Perspectives, Part II
Discussion Leader: Anthony Nicholls (OpenEye Scientific Software, Santa Fe, NM, USA)
8:30 pm - 9:15 pm Cosma Shalizi (Statistics Department, Carnegie Mellon University, and the Santa Fe Institute)
"Simple Simulation Methods for Quantifying Uncertainty"
9:15 pm - 9:30 pm Discussion
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 10:30 amPractical Statistics, Part II
Discussion Leader: Haihong Ni (BioDuro, Beijing, China)
9:00 am - 9:15 am Martha S. Head (GSK, Upper Merion, PA, USA)
"One of these things is not like the others?"
9:15 am - 9:20 am Discussion
9:20 am - 9:35 am Paul Czodrowski (Merck KG, Germany)
"The Kappa Statistic: Taking Care of Background Rates"
9:35 am - 9:40 am Discussion
9:40 am - 10:00 am Short Poster Presentations
10:00 am - 10:30 am Coffee Break
10:30 am - 12:30 pmDeeper Issues for Statistics in CADD: NULL Models
Discussion Leader: Anna Linusson (Umeå University, Umeå, Sweden)
10:30 am - 11:15 am Woody Sherman (Schrödinger, New York, NY, USA)
"Null Models to Improve Assessment of Virtual Screening Enrichments and Lead Optimization Scoring"
11:15 am - 11:30 am Discussion
11:30 am - 12:15 pm Marcel Verdonk (Astex Pharmaceuticals, UK)
"Statistics don't lie. Or do they?"
12:15 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 6:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 8:30 pmStatistics and Societal Issues, Part III
Discussion Leader: Glen Kellogg (VCU, Richmond, VA, USA)
7:30 pm - 8:15 pm Greg Landrum (Novartis, Basel, Switzerland)
"Is That a Scientific Report or Just Some Cool Pictures from the Lab? Reproducibility and Computational Chemistry"
8:15 pm - 8:30 pm Discussion
8:30 pm - 9:30 pmExternal Perspectives, Part III
Discussion Leader: Anthony Nicholls (OpenEye Scientific Software, Santa Fe, NM, USA)
8:30 pm - 9:15 pm Elizabeth Iorns (CEO, Science Exchange, Palo Alto, CA, USA)
"The Reproducibility Initiative: a Potential Solution to the Irreproducibility Problem"
9:15 pm - 9:30 pm Discussion
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 10:30 amPractical Statistics, Part III
Discussion Leader: Haihong Ni (BioDuro, Beijing, China)
9:00 am - 9:15 am Ullrika Sahlin (Lund University, Lund, Sweden)
"Uncertainty in QSAR Predictions - Bayesian Inference and the Magic of Bootstrap"
9:15 am - 9:20 am Discussion
9:20 am - 9:35 am Stephen Johnson (BMS, Princeton, NJ, USA)
"How to Measure to Anything"
9:35 am - 9:40 am Discussion
9:40 am - 9:55 am Eric Martin (Novartis, San Francisco, CA, USA)
"Hamming Distance and Hemple's Ravens: How to Build a Euclidean Property Space from Sparse Binary Fingerprints"
9:55 am - 10:00 am Discussion
10:00 am - 10:30 am Coffee Break
10:30 am - 12:30 pmDeeper Issues for Statistics in CADD: Parameters
Discussion Leader: Ajay Jain (UCSF, San Francisco, CA, USA)
10:30 am - 11:15 am Kim Branson (Hessian Informatics, Emerald Hills, CA, USA)
"Curb Your Enthusiasm with Bayes Factors"
11:15 am - 11:30 am Discussion
11:30 am - 12:15 pm Vijay Pande (Stanford, Palo Alto, CA, USA)
"Less Art, More Science: A Systematic, Reproducible, Statistically Significant Scheme for Parameterizing Force Fields"
12:15 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 6:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
Nominations for the next Vice Chair; Fill out Conference Evaluation Forms; Discuss future Site & Scheduling preferences; Election of the next Vice Chair
7:30 pm - 8:30 pmStatistics and Societal Issues, Part IV
Discussion Leader: Yvonne Martin (AbbVie, Chicago, IL, USA)
7:30 pm - 8:15 pm Alex Tropsha (UNC, Chapel Hill, NC, USA)
"What to Expect When you are Expecting... the Editorial Decision on your Manuscript?"
8:15 pm - 8:30 pm Discussion
8:30 pm - 9:30 pmExternal Perspectives, Part IV
Discussion Leader: Anthony Nicholls (OpenEye Scientific Software, Santa Fe, NM, USA)
8:30 pm - 9:15 pm Carson Chow (NIH/NIDDK, Bethesda, MD, USA)
"Bayesian methods for parameter estimation and model comparison"
9:15 pm - 9:30 pm Discussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 10:30 amPractical Statistics, Part IV
Discussion Leader: Haihong Ni (BioDuro, Beijing, China)
9:00 am - 9:15 am Gareth Jones (Arena Pharmaceuticals, San Diego, CA, USA)
"Use of Levenberg-Marquardt Fitting for Dose-Response Data"
9:15 am - 9:20 am Discussion
9:20 am - 9:35 am Istvan Enyedy (Biogen Idec, Boston, MA, USA)
"The Statistics of Virtual Screening and Lead Optimization"
9:35 am - 9:40 am Discussion
9:40 am - 9:55 am Scott Brown (Sunovion Pharmaceuticals, Woburn, MA USA)
"Analysis in the Presence of Experimental Error - How Good Should You Be?"
9:55 am - 10:00 am Discussion
10:00 am - 10:30 am Coffee Break
10:30 am - 12:30 pmDeeper Issues for Statistics in CADD: Experimental Data
Discussion Leader: Pat Walters (Vertex Pharmaceuticals, Boston, USA)
10:30 am - 11:00 am John Chodera (Memorial Sloan-Kettering Cancer Center, NY, NY, USA)
"Experimental (T)error: Strategies for Coping with Data in an Uncertain World - Part 1"
11:00 am - 11:30 am Terry Stouch (Science for Solutions, Princeton, NJ, USA)
"Experimental (T)error: Strategies for Coping with Data in an Uncertain World - Part 2"
11:30 am - 12:00 pm Discussion
12:00 pm - 12:25 pm Nathan Baker (Pacific Northwest National Laboratory, Richland, WA, USA)
"The Importance of Metadata in Preserving and Reusing Scientific Information"
12:25 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 6:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II
6:00 pmDinner
7:30 pm - 8:30 pmStatistics and Societal Issues, Part V
Discussion Leader: Anthony Nicholls (OpenEye Scientific Software, Santa Fe, NM, USA)
7:30 pm - 8:30 pm General Discussion: Future Directions in Applying Statistics in Molecular Design
8:30 pm - 9:30 pmExternal Perspectives, Part V
Discussion Leader: Anthony Nicholls (OpenEye Scientific Software, Santa Fe, NM, USA)
8:30 pm - 9:15 pm George Wolford II (Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA)
"Finding Patterns- A Fish Story"
9:15 pm - 9:30 pm Discussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture

Funding for this conference was made possible (in part) by 1 R13 GM 106462-01 from The National Institute of General Medical Sciences. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.

 
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