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2008 Bottleneck Agenda

2008 NIGMS PSI Bottlenecks Workshop
April 14-16, 2008
Natcher Conference Center, NIH
Conference Room E

 

Monday, April 14

7:15 am Refreshments and Poster Setup

7:55 am Opening Remarks - John Norvell and Jeremy Berg

Session I Homology Modeling in Structural Genomics
Chair: Ward Smith

8:00 am Keynote Lecture, A TALE OF TWO SPACES: STRUCTURE MEETS SEQUENCE
Dr. Michael Levitt, Stanford University (01_Levitt)

8:50 am MODELING PROTEIN SEQUENCE SPACE WITH ALL PDB STRUCTURES AS TEMPLATES
Diana Murray
, Columbia University (02_Murray)

9:15 am DEVELOPMENT OF SCWRL4 FOR IMPROVED PREDICTION OF PROTEIN SIDE-CHAIN CONFORMATIONS
Georgy Krivov,
Fox Chase Cancer Center, Philadelphia (03_Krivov)

9:40 am DISTANCE MATRIX-BASED APPROACH TO PROTEIN STRUCTURE PREDICTION
Andrzej Kloczkowski
, Iowa State University (04_Kloczkowski)

10:05 am 20 minute Coffee Break and Poster Viewing

10:25 am MULTIPLE MAPPING METHOD WITH MULTIPLE TEMPLATES FOR HOMOLOGY MODELING
András Fiser,
Albert Einstein College of Medicine (05_Fiser)

10:50 am COMPARATIVE PROTEIN STRUCTURE MODELING FOR MOLECULAR REPLACEMENT IN X-RAY CRYSTALLOGRAPHY
Ursula Pieper, University of California at San Francisco (06_Pieper)

11:15 am BEYOND RMSD: HOMOLOGY MODEL ACCURACY FROM AN APPLICATIONS PERSPECTIVE
Roberto Sanchez,
Mount Sinai School of Medicine, New York (07_Sanchez)

11:40 am Geometric potential for protein structure and binding prediction
Jie Liang, University of Illinois at Chicago (08_Liang)

12:05 pm 60 minute Lunch
Session I speakers at Designated Tables in Cafeteria
Session II speakers in Designated Tables in Cafeteria

Session II Data, Databases and Knowledge
Chair: Ashley Deacon

1:15 pm THE PSI STRUCTURAL GENOMICS KNOWLEDGEBASE
Helen M. Berman,
The State University of New Jersey (09_Berman)

1:40 pm THE PSI KNOWLEDGEBASE PROTEIN MODEL PORTAL
Torsten Schwede,
Biozentrum University of Basel, Switzerland (10_Schwede)

2:05 pm TOPSAN: A community-driven resource for enhanced impact of structural genomics data
Sri Krishna Subramanian, University of California (11_Subramanian)

2:30 pm PSI DATA MANAGEMENT AND REPORTING: EXPECTATIONS, STANDARDS, AND UTILITY
J. Michael Sauder, SGX Pharaceuticals, Inc., San Diego (12_Sauder)

2:55 pm 20 minute Coffee break

3:15 pm INTEGRATION OF MASS SPECTROMETRY WITH HIGH-THROUGHPUT PROTEIN CRYSTALLOGRAPHY
Tarun Gheyi
, New York SGX Research Center for Structural Genomics (13_Gheyi)

3:40 pm CRYSTALLIZATION IMAGE ANALYSIS ON THE WORLD COMMUNITY GRID
Christian A. Cumbaa, Ontario Cancer Institute, Toronto (14_Cumbaa)

4:05 pm QUALITY OF PROTEIN CRYSTAL STRUCTURES IN THE PDB
S. Ramaswamy, The University of Iowa (15_Ramaswamy)

4:40 pm 10 minute Coffee Break

 

Session III An International Perspective on Structural Genomics

4:50 pm STRUCTURAL PROTEOMICS PROJECTS IN JAPAN
Shigeyuki Yokoyama, University of Tokyo, Japan (16_Yokoyama)

5:25 pm Session Close

6:30 pm Dinner at Centro Italian Grill, 4838 Bethesda Avenue, Bethesda, MD 20814  

Tuesday, April 15

7:15 am Refreshments and Poster Viewing

Session IV Mini-Session - Targeting for Success
Chair: Brian Fox

8:00 am ADDRESSING PROTEIN CRYSTALLIZATION BOTTLENECKS BY SCREENING MULTIPLE HOMOLOGUES
Lukasz Jaroszewski, University of California San Diego (17_Jaroszewski)

8:25 am DATAMINING STRUCTURE SOLUTION DETERMINANTS IN THE NESG PIPELINE
W. Nicholson Price,
NESG (18_Price)

8:50 am THERMOPHILLIC EUKARYOTES AS A SOURCES FOR STRUCTURAL GENOMIC TARGETS
Craig A. Bingman,
University of Wisconsin-Madison (19_Bingman)

9:15 am HIGH-THROUGHPUT STRUCTURAL PROTEOMICS
Nathaniel Echols,
UC Berkeley (20_Echols)

9:40 am The Medical structural Genomics of Pathogenic Protozoa (MSGPP) PROTEIN PRODUCTION pipeline
Alberto Napuli, University of Washington (21_Napuli)

10:05 am 20 minute Coffee Break and Poster Viewing

Session V Mini-Session -High Throughput NMR Methods

10:25 am INTEGRATION OF FAST DATA COLLECTION AND AUTOMATED PROBABILISTIC ASSIGNMENTS FOR PROTEIN NMR SPECTROSCOPY
Arash Bahrami,
University of Wisconsin-Madison (22_Bahrami)

10:50 am IMPACT OF PROTEIN-DETERGENT INTERACTIONS ON NMR STRUCTURE DETERMINATION
Linda Columbus,
University of Virginia (23_Columbus)

11:15 am Characterization of Protein Detergent Complexes
Witek Kwiatkowski, The Salk Institute for Biological Studies (24_Kwiatkowski)

11:40 am LINKING MACHINE VISION WITH CRYSTAL HARVESTING ROBOTICS
Robert Viola,
Square One Systems Design, Inc. (25_Viola)

12:05 pm 60 minute Lunch
Session III speakers at Designated Tables in Cafeteria
Session IV speakers in Designated Tables in Cafeteria

Session VI Traditional Bottlenecks
Chair: Celia Goulding
1:15 pm GFP-BASED MEMBRANE PROTEIN OVEREXPRESSION AND PURIFICATION IN E. COLI AND S. CEREVISIAE
Hyun Kim, Stockholm University, Sweden (26_Kim)

1:40 pm Heterologous Expression of L. major proteins in S. cerevisiae
Elizabeth J. Grayhack, University of Rochester Medical School (27_Grayhack)

2:05 pm SALVAGE METHODS APPLIED TO FAILED PFAM FAMILIES
Scott Lesley, The Joint Center for Structural Genomics (28_Lesley) 

2:30 pm MICROFLUIDIC PLATFORMS FOR (MEMBRANE) PROTEIN CRYSTALLIZATION
Paul J.A. Kenis,
University of Illinois at Urbana-Champaign (29_Kenis)

2:55 pm 20 minute Coffee Break and Poster Viewing

3:15 pm A SEMI-AUTOMATED SYSTEM for NANOVOLUME PLUG-BASED CRYSTALLIZATION
Cory Gerdts, deCODE Biostructures, Inc. (30_Gerdts)

3:40 pm integratIng HT EmpricAl data with HT CRYSTALLIZATION
Joseph R. Luft, The Center for High-Throughput Structural Biology (31_Luft)

4:05 pm FIXING MISFIT SIDE CHAINS: MOLPROBITY & REAL-SPACE REFINEMENT -
Jeffrey J. Headd, Duke University (32_Headd)

4:30 pm EXPLORING QPCR-DERIVED THERMAL MELTS FOR LIGAND SCREENING -
Amanda Meyer, Albert Einstein College of Medicine (33_Meyer)

4:55 pm Extracting and expanding information derived from ~½ a million classified crystallization images
Edward H. Snell,
The Center for High-Throughput Structural Biology (34_Snell)

5:20 pm End Session

5:30 - 7 PM Standby Poster Session
5:30 - 6:15 pm Odd number authors standby
6:15 - 7:00 pm Even number authors standby

 

Wednesday, April 16

7:15 am Refreshments and Poster Viewing

Session VII The Really Hard Stuff
Chair: Lance Stewart

8:00 am DISCOVERY-ORIENTED EUKARYOTIC INTEGRAL MEMBRANE PROTEIN PRODUCTION
Franklin A. Hays,
University of California San Francisco (35_Hays)

8:25 pm EXPRESSION, PURIFICATION, AND ASSEMBLY OF FUNCTIONAL HUMAN MEMBRANE STEAROYL-COA DESATURASE COMPLEX USING CELL-BASED AND CELL-FREE TECHNOLOGIES
Brian Fox,
University of Wisconsin - Madison (36_Fox)

8:50 am Detergent Screening Via Immobilized-Protein Stability Assay
James M. Vergis, University of Virginia Health Sciences Center (37_Vergis)

9:15 am AUTOMATED, HIGH-THROUGHPUT PLATFORM FOR SOLUBLE DOMAIN SCREENING
Pawel Listwan, Los Alamos National Laboratory (38_Listwan)

9:40 am A CHOLESTEROL BIOSYNTHETIC YEAST FOR MAMMALIAN MEMBRANE PROTEIN PRODUCTION
Niall J. Fraser, Univesity of Glasgow, Scotland (39_Fraser)

10:05 am 20 minute Coffee Break and Poster Take-Down

10:25 am PSI MATERIALS REPOSITORY: GOALS AND PROGRESS
Joshua LaBaer, Harvard Institute of Proteomics (40_LaBaer)

10:50 am LOGISTICAL CONSIDERATIONS FOR PARTICIPATION IN THE PSI-MR
John G. Primm, University of Wisconsin-Madison (41_Primm)

11:15 am GETTING DOWN AND DIRTY WITH DETERGENTS: QUANTITATION, SYNTHESIS, AND SCREENING
Philip D. Laible,
Argonne National Laboratory (42_Laible)

11:40 am USING DETERGENT PHASE BOUNDARIES TO CRYSTALLIZE MEMBRANE PROTEINS
Michael G. Malkowski,
The Center for High-Throughput Structural
Biology (43_Malkowski)

12:05 pm End

12:20 pm Lunch - Organizers have a final meeting

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health