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:
- Session 1: Dev Thirumalai, University of Maryland
; Vijay Pande, Stanford
- Session 2: William Eaton, NIH; Teresa Head-Gordon, UC Berkeley
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.