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 IBM-SDSC Protein Folding Workshop, March 30-31, 2001 On Friday and Saturday, March 30 and 31, 2001, the IBM Blue Gene project and the San Diego Supercomputer Center hosted a two-day Protein Folding Workshop on the campus of the University of California at San Diego. The full text of the workshop announcement is available here and the organizers can be contacted via e-mail. A detailed agenda may be found here. The workshop brought together distinguished researchers in the area of protein folding to help stimulate interactions between the various communities (theoretical, experimental, and simulation) involved. The workshop comprised invited talks, contributed posters and breakout sessions. There were 12 invited talks organized into three sessions that addressed experimental approaches, computer simulation applications and techniques, and developments in biophysical theory, each as they relate to protein folding. The breakout sessions provided a forum for discussion about suggestions for new avenues of research and collaboration both for the IBM Blue Gene project and for the protein science community at large. A number of posters were contributed by the participants (see below). The workshop web site contains additional information about the conference. This workshop was a satellite meeting of the American Chemical Society National Meeting, which met from April 1-5, 2001 in San Diego. The organizers of the protein science workshop wish to acknowledge the help of Prof. Charles Brooks, III, of The Scripps Research Institute and Kim Baldridge, of the San Diego Supercomputer Center, in organizing this meeting. Detailed schedule for the meeting: Day 1: Friday, March 30, 2001, "Institute of the Americas" building on the UCSD campus 8:00-8:30AM Registration and coffee 8:30-8:45AM Welcome, meeting objectives, introductions - Joseph Jasinski, IBM  Biophysical theory session 8:45-9:05AM Biophysical theory overview - Kevin Plaxco, UC Santa Barbara  9:05-9:45AM Biophysical talk 1 - Peter Wolynes, UC San Diego  9:45-9:55AM Q+A 9:55-10:35AM Biophysical talk 2 - Eugene Shakhnovich, Harvard University  10:35-10:45AM Q+A 10:45-11:00AM Break 11:00-11:40AM Biophysical talk 3 - Jose Onuchic, UC San Diego 11:40-11:50AM Q+A 12:00-1:00PM Lunch 1:00-2:00PM Posters 2:00-4:00PM Two simultaneous breakout sessions:
6:00-7:00PM Buffet dinner Experimental session - part 1 7:00-7:20PM Experimental overview - Chris Dobson, Cambridge University 7:20-8:00PM Experimenal talk 1 - Peter Wright, The Scripps Research Institute 8:00-8:10PM Q+A 8:10-8:50PM Experimental talk 2 - Heinrich Roder, Fox Chase Cancer Center 8:50-9:00PM Q+A 9:00-11:00PM Posters and reception Day 2: Saturday, March 31, 2001, "Institute of the Americas" building on the UCSD campus Experimental session - part 2 8:30-9:10AM Experimental talk 3 - William Eaton, National Institutes of Health  9:10-9:20AM Q+A Simulation session - part 1 9:20-9:40AM Simulation overview - Wilfred van Gunsteren, ETH 9:40-10:20AM Simulation talk 1 - Peter Kollman, UC San Francisco  10:20-10:30AM Q+A 10:30-10:45AM Break 10:45-11:25AM Simulation talk 2 - Vijay Pande, Stanford 11:25-11:35AM Q+A 11:35AM-12:05PM SDSC overview - Fran Berman, SDSC  12:05-12:30PM Report from breakout groups 1+2, about 10 minutes each 12:30-2:00PM Lunch Simulation session - part 2 2:00-2:40PM Simulation talk 3 - Charlie Brooks, III, The Scripps Research Institute  2:40-2:50PM Q+A 3:00-5:00PM Posters 6:00-8:00PM Reception and banquet at the DoubleTree hotel, wrap-up Poster Presentations 1.BlueGene Hardware Design, Monty Denneau, Ruud Haring & BlueGene Team, IBM T. J. Watson Research Center, PO Box 218, Route 134, Yorktown Heights, NY 10598 2.Blue Gene System Software, George Almasi, Jose Brunheroto, Calin Cascaval, José Castaños  , Paul Crumley, Wilm Donath, Maria Eleftheriou, Manish Gupta, Lorraine Herger, Derek Lieber, José Moreira, Matt Newton, Richard Regan, Alda Sanomiya and Hank Warren IBM T. J Watson Research Center, PO BOX 218, Yorktwon Heights, NY 105983.Validation of BlueMatter: a molecular dynamics software package for Blue Gene, Robert Germain  , Blake Fitch   et al, IBM T. J Watson Research Center, PO BOX 218, Yorktwon Heights, NY 105984.Electrostatics of pH-dependent local folding of an alpha helix in GART, Dimitrios Morikis, Department of Chemistry and Biochemistry, UCSD, La Jolla, CA 92093 5.A new effective potential to address desolvation in protein folding, Margaret Cheung, Physics Department, University of California, San Diego, La Jolla, CA 92093 6.Hierarchy of Protein Motion and Folding, Anton Feenstra , Biophysical Chemistry, Nijenborgh 4, 9747 AG Groningen, The Netherlands7.Thermal unfolding of DHFR: molecular modeling, Yuk Sham et al, IBM T. J. Watson Research Center, PO Box 218, Route 134, Yorktown Heights, NY 10598 8.Analysis of a ten-nanosecond molecular dynamics simulation of mouse acetylcholinesterase, Kaihsu Tai, Dept of Chem. & Biochem. UCSD, 9500 Gilman Dr, La Jolla CA 92093-0365 9.Identifying Native-Like Protein Structures using Physically-Derived Molecular Potentials, Brian N. Dominy, The Scripps Research Institute, Department of Molecular Biology, 10555 N. Torrey Pines Road, TPC-6 10.Protein Folding Simulations by Generalized-Ensemble Algorithms, Yuko Okamoto, Department of Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan 11.Protein Science Visualization, Frank Suits and Donna Gresh  , IBM Hawthorne, 30 Saw Mill River Rd. Hawthorne, NY 1053212.Novel symplectic quaternion rigid body integrator for molecular dynamics, Thomas Miller, Pratap Pattnaik, Antony Ndirango, Maria Eleftheriou  , Dennis Newns  and Glenn Martyna , IBM T. J. Watson Research Center, PO Box 218, Route 134, Yorktown Heights, NY 1059813.A New Linear Interaction Approximation Method for Binding Affinity Calculation Based on Continuum Solvent Model, Ruhong Zhou  , Richard Friesner, Robert Rizzo and William Jorgensen, IBM Thomas J. Watson Research Center, PO Box 218, Route 134, Yorktown Heights, NY 1059814.Accelerated Protein Folding Simulation of Three Small Proteins by The Self-Guided Poisson-Boltzmann Molecular Dynamics Simulation, Ray Luo, Box 0446 Dept. Pharm. Chem., UCSF, 513 Parnassus Ave, San Francisco, CA 94143-0446 15. Hybrid simulations of the BAH-HI endonuclease enzymatic reaction.Wanda Andreoni, Tiziana Jonas-Mordasini, and Alessandro Curioni, IBM Zurich Research Laboratory, Saeumerstrasse 4, CH-8813 Rueschlikon, Switzerland 16.Protein structure prediction at CASP4, Ajay Royyuru et al, IBM T. J. Watson Research Center, PO Box 218, Route 134, Yorktown Heights, NY 10598 17.Hydrophobic Ratio: a new indicator for protein native structures and its application in molecular dynamics, B. D. Silverman et al, IBM T. J. Watson Research Center, PO Box 218, Route 134, Yorktown Heights, NY 10598 18.Field-Based Similarity Searching and Alignment of Flexible Molecules, Mike C. Pitman  et al, IBM T. J. Watson Research Center, PO Box 218, Route 134, Yorktown Heights, NY 1059819.A Computer the Size of Planet Earth, Steve Elbert, et al. Entropian, Inc., 4350 Executive Drive, Suite 200, San Diego, CA 92121 Related Photos    William Swope (IBM), Michael Pitman (IBM), Charlie Brooks (The Scripps Research Institute), Arthur Voter (Los Alamos National Labs) 
Click on the camera  for attendee photographs. |
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