Report on the collaborative project
between ICOT and the NIH


Richard J. Feldmann
Division of Computer Research and Technology
National Institutes of Health
Bethesda, Maryland 20892

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Dr. Michaels expects that in the next year there will be fragments of about 50 
genomes for various small organisms entered into the GenoGraphics format. Geno-
Graphics as a result of Dr. Hagstrom's work is now written in C and runs on any PC 
compatible machine. We expect that GenoGraphics will become a world standard tool 
for the representation, manipulation and investigation of genomes. 

The collaboratory model which George Michaels has developed is a powerful out-
come of our interaction with ICOT and the other US national laboratories. Scientific 
workers can now come together from all over the world and using the InterNet can 
work together effectively for a short period of time. 

In the Protein Folding portion of our collaboration with ICOT we have built and 
analyzed several models for the representation of protein structure. The collection and 
analysis of x-ray crystallographic data sets was begun in our laboratory almost 20 years 
ago. The relationships between protein structure, function and folding pathway have 
been very difficult to elucidate. The protein folding problem is the key technology 
which will enable biological system design. During the collaborative project workers in 
both countries engaged in the design and construction of both physical and computer 
models. Physical models provide simple, visual, trans-cultural vehicles for communica-
tion. Computer models can be constructed to represent salient features of the physical 
models. Using both logic programming and conventional machines we have investi-
gated the statistics and dynamics of these models. The resolution of a protein model 
and its water environment is a critical determinant of the computer power required to 
simulate folding. Parallel computational techniques for simulating protein folding using 
logic programming machines have been developed by our ICOT collaborators, Makoto 
Hirosawa, Masato Ishikawa and Masaki Hoshida. Hirosawa-san spent his whole winter 
vacation programming and running the folding algorithm. At the NIH, David Rawn 
(Towson State University) and I have made progress towards finding a topological prin-
ciple which unites the water seeking (hydrophilic) and water avoiding (hydrophobic) 
aspects of protein structure. A complete and simple topological model would reduce 
the N2 portion calculations to the number of amino acids in a given protein. With such 
a model we would hope to be able to fold proteins on many different types of computers. 

Discussion with the ICOT workers has also focused on computer languages, style 
of operating environment and network connectivity. Using the PSI II and III machines 
loaned to the NIH under the auspices of this collaboration, it has been possible to 
evaluate the state of development of the hardware and software produced by the Fifth 
Generation Project. Any user who decided to accept a research machine must know 
that it will be a lot of work. The FGCS conference shows that at the end of the project, 
much more of the potential of the hardware and software is now usable. During the 
continuation year we at the NIH would expect to make much greater use of the capa-
bilities of the PIM machines at ICOT. Discussions during the conference brought out 


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