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Computer Aided Drug Design
Gordon Research Conference

Experiment Meets Modeling: Where Are We Now, Where Are We Going

Dates

July 19-24, 2009

Location

Tilton School
Tilton, NH

Organizers

Chair:
Brian Shoichet

Vice Chair:
Gerhard Klebe

Meeting Description

The Gordon Research Conference on Computer-Aided Drug Design, which began its life as the QSAR GRC, has been held every second year since the early 1970s. The conference brings together industrial, academic and government scientists working on computational simulation of ligands and their targets. Because computer-aided drug design covers a wide field of research, each conference focuses on topical areas of innovation and progress, supporting a dynamic atmosphere. A focus for the 2009 conference will on how computational and experimental methods inform each other in current research problems. Topics will include recent exciting advances in protein design and modeling, the role of water in modeling ligand-protein binding, understanding thermodynamics and kinetics of ligand binding, protein and ligand-based networks in biology and pharmacology, and the problems and opportunities presented by the chemical and biological spaces in which ligand design occurs. The CADD GRC continues to offer speakers and participants generous speaking and discussion periods. Discussion sessions are lively and controversy is welcomed; it is a condition of their invitation that speakers give talks on largely unpublished, cutting edge results.

The meeting will again be held in Tilton School NH, where we have been happily accommodated for several years. All conferees are encouraged to present posters; twenty-four presenters will be invited to give short talks to introduce their material. This meeting is typically oversubscribed, and we encourage submission of applications by early 2009. Participants will be a mix of researchers from industry, academia, and government, of different ages, backgrounds, and countries. Despite the popularity of the conference, students, postdocs, and young investigators new to the field should not hesitate to apply.

Contributors

Meeting Program

SUNDAY
2:00 pm - 9:00 pmArrival and Check-in (Office Closed 6:00 pm - 7:00 pm)
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pmSuccess Stories from Drug Design
Discussion Leader: Hugo Kubinyi (Univ. Heidelberg, Germany)
7:40 pm - 8:20 pm Jay Pandit (Pfizer, Groton, USA)
"The PDE-family"
8:20 pm - 8:35 pm Discussion
8:35 pm - 9:15 pm Sandra Cowan-Jacob (Novartis, Basel, Switzerland)
"Structural Biology of Abl kinase: discovering drugs to overcome imatinib resistance in chronic myelogenous leukemia"
9:15 pm - 9:30 pm Discussion
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 11:30 amThe Ribosome as a Drug Target
Discussion Leader: Holger Gohlke (Univ. Düsseldorf, Germany)
9:00 am - 9:40 am Tom Steitz (Yale-Univ., New Haven, USA)
"Targeting the Ribosom"
9:40 am - 10:00 am Discussion
10:00 am Coffee Break / Group Photo
10:30 am - 11:10 am Erin Duffy (Rib-X, New Haven, USA)
"Development of clinical candidates for RNAs"
11:10 am - 11:30 am Discussion
11:30 am - 12:30 pmOpen Mic Session (5 minute talks by poster presenters)
11:30 am - 11:35 amDavid Case (Rutgers University)
"Implicit Solvent Rescoring in Ligand-Receptor Docking"
11:35 am - 11:40 amJindrich Fanfrlik (UOCHB)
"Protein-Ligand Scoring: A Challenge For Semiempirical Quantum Chemical Methods"
11:40 am - 11:45 amRafaela Ferreira (University of California, San Francisco)
"Docking vs. Screening against Cruzain"
11:45 am - 11:50 amXinjun Hou (Pfizer)
"Beyond Rule of Five: A CNS Multi Parameter Optimization (MPO) Tool"
11:50 am - 11:55 amJohn Irwin (UCSF)
"Are automatic docking screens feasible?"
11:55 am - 12:00 pmHiqmet Kamberaj (University of Minnesota)
"Computational Alanine Scanning of the BLIP/TEM-1 complex"
12:00 pm - 12:05 pmPeter Kolb (University of California, San Francisco)
"Structure-based discovery of beta2-adrenergic receptor ligands"
12:05 pm - 12:10 pmDmytro Kozakov (Boston University)
"Prediction of druggable hotspots on PPI interfaces using FTMap algorithm"
12:10 pm - 12:15 pmMichael Lajiness (Eli Lilly & Company)
"Mobius: Integrating Information to support Small Molecule Drug Discovery"
12:15 pm - 12:20 pmMelissa Landon (Brandeis University)
"Identification of stabilizing agents of Uch-L1 by structure-based strategies"
12:20 pm - 12:25 pmKlaus Liedl (University of Innsbruck)
"Prediction of Entropy Relying on Phase Space Inhomogeneities"
12:25 pm - 12:30 pmSamy Meroueh (Indiana University School of Medicine)
"Computational design of urokinase receptor modulators"
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 9:30 pmRNA and Aptamers in Drug Research
Discussion Leader: Jennifer Krumrine (AstraZeneca)
7:30 pm - 8:10 pm Kevin Sanbonmatsu (Los Alamos National Laboratory, New Mexico, USA)
"Drug landing zones on the ribosome: non-specific binding and stochastic gating in the decoding center"
8:10 pm - 8:30 pm Discussion
8:30 pm - 9:10 pm Thomas Hermann (UCSD, San Diego, USA)
"RNA as a drug target"
9:10 pm - 9:30 pm Discussion
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmThermodynamics and Ligand Binding
Discussion Leader: Jeremy Tame (Yokohama City University, Japan)
9:00 am - 9:40 am John Ladbury (Houston, Texas, USA)
"Thermodynamic input to drug development: false panacea or pipeline dream?"
9:40 am - 10:00 am Discussion
10:00 am Coffee Break
10:30 am - 11:10 am Steve Homans (Univ. of Leeds, UK)
"Thermodynamic Decomposition - What can it tell us about the driving forces for ligand binding?"
11:10 am - 11:30 am Discussion
11:30 am - 12:10 pm Glyn Williams (Astex, Cambridge, UK)
"Exploring Chemical and Thermodynamic Space Using Fragments"
12:10 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 8:30 pmSelectivity and Residence Time
Discussion Leader: Katharine Holloway (Merck, USA)
7:30 pm - 8:10 pm Helena Danielson (Univ. of Uppsala, Sweden)
"SPR biosensor generated interaction kinetic data for identification and design of leads: Applications to HIV drug discovery"
8:10 pm - 8:30 pm Discussion
8:30 pm - 9:30 pmOpen Mic Session (5 minute talks by poster presenters)
8:30 pm - 8:35 pmPrasenjit Mukherjee (Novartis Institute of Biomedical Research)
"Surrogate Autoshim and Profile QSAR: Two predictive methods for early lead discovery"
8:35 pm - 8:40 pmNoel O'Boyle (Cambridge Crystallographic Data Centre)
"Why multiple scoring functions can improve docking performance"
8:40 pm - 8:45 pmJohn Overington (EMBL-EBI)
"ChEMBL - Large-scale Open Access Data for Drug Discovery"
8:45 pm - 8:50 pmOlli Pentikainen (University of Jyvaskyla)
"Protein structure-based shape comparison in ligand discovery"
8:50 pm - 8:55 pmPatrik Rydberg (University of Copenhagen)
"Fast Prediction of Cytochrome P450 Mediated Drug Metabolism"
8:55 pm - 9:00 pmJochen Schlosser (University of Hamburg)
"TrixX BMI and the Economy of Time: Index-Driven Structure-Based Lead Identification"
9:00 pm - 9:05 pmKatherine Shaw (University of Bristol)
"Developing QM/MM methods for binding free energy predictions"
9:05 pm - 9:10 pmYao Shen (University of Notre Dame)
"Targeting the type II fatty acid synthetic pathway - Design of new antibiotics"
9:10 pm - 9:15 pmKatrin Spiegel (Novartis)
"Boosting enrichment factors via induced fit ensemble docking"
9:15 pm - 9:20 pmGudrun Spitzer (University of Innsbruck)
"Shape based Screening and Thermodynamic Characterization of Minor Groove Ligands"
9:20 pm - 9:25 pmOlaf Wiest (University of Notre Dame)
"CAMD Studies of HDAC Inhibitors"
9:25 pm - 9:30 pmAnthony Nichols (Openeye Inc.)
"A Community Structure-Activity Resource"
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmMerging Chemical and Biological Space
Discussion Leader: Ruben Abagyan (Scripps, San Diego)
9:00 am - 9:40 am Jean-Louis Reymond (Univ. of Berne, Switzerland)
"What is contained in chemical space"
9:40 am - 10:00 am Discussion
10:00 am Coffee Break
10:30 am - 11:10 am Christine Orengo (Univ. London, UK)
"Predicting functional families and functional networks to identify putative drug targets"
11:10 am - 11:30 am Discussion
11:30 am - 12:10 pm Jordi Mestres (MIMI, University Pompeu Fabra, Spain)
"Drug polypharmacology in complex diseases"
12:10 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 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 - 9:30 pmProtein Networks and Systems Biology
Discussion Leader: Tanja Kortemme (UCSF, San Francisco, USA)
7:30 pm - 8:10 pm Hans-Werner Mewes (TU München, Germany)
"Systems Biology as a Paradigm for Therapy and Drug Development"
8:10 pm - 8:30 pm Discussion
8:30 pm - 9:10 pm Patrick Aloy (Barcelona Science Park, Spain)
"Protein interaction specificity: Using 3D structures to unveil compensatory effects in protein interaction networks"
9:10 pm - 9:30 pm Discussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmElectrostatics as a Major Obstacle in Computational Drug Design
Discussion Leader: Curt Breneman (Rensselaer Polytech. Inst., USA)
9:00 am - 9:40 am Jens-Eric Nielsen (Univ. of Dublin, Ireland)
"The perturbation of pKa values in proteins and protein-ligand complexes"
9:40 am - 10:00 am Discussion
10:00 am Coffee Break
10:30 am - 11:10 am Thomas Simonson (Ecole Polytechnique, Dept of Biology, Paris, France)
"Probing charge interactions with free energy simulations?"
11:10 am - 11:30 am Discussion
11:30 am - 12:10 pm Jay W. Ponder (Washington Univ., St. Louis, USA)
"Charge Models and Polarizable Force Fields for Protein-Ligands Complexes"
12:10 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II
6:00 pmDinner
7:30 pm - 9:30 pmKeynote: Water as a Major Obstacle in Computational Drug Design
Discussion Leader: Kathryn Loving (Schrodinger, Inc., New York, USA)
7:30 pm - 8:10 pm Gerhard Hummer (National Institutes of Health, Bethesda, USA)
"The role of water in protein-ligand binding"
8:10 pm - 8:30 pm Discussion
8:30 pm - 9:10 pm Ken Dill (UCSF, San Francisco, USA)
"Towards improved computational models of water"
9:10 pm - 9:30 pm Discussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDepart
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