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Understanding of this
process would also represent understanding of the code in the one
dimensional DNA molecules becomes the three dimensional form that we call
life, would allow us to interpret the output of the human genome project
and other genome projects, and improve our ability to design drugs by
seeing the three dimensional molecular details of the proteins in our
bodies (with which almost all kinds of drug interact). At present, such
bottlenecks as the inability to read the human genome, and understand it in
terms of protein structure and function, are prohibiting the development of
major health care applications and pharmaceutical markets.
Proteins are also interesting as useful molecules themselves, not just as
targets for drugs. The biotechnology industry is primarilly concerned in
producing proteins, ideally including novel proteins, as therapeutics.
However, since proteins can also be made synthetically, by purely chemical
methods, and fold up spontaneously according to the message in the sequence
of amino acid residues which comprises them, a deeper understanding of how
such preprogrammed chains of atoms fold up might have have profound
effect for all industry. It would allow us not only to design novel
proteins, but also novel polymers and smart new materials. Ultimately this
could also include a more practical approach to designing and producing
those tiny machines and molecular-scale computer chips and storrage devices
envisaged by nanotechnology.
The team is drawn from many research and related divisions of IBM
including several groups at the T.J..Watson Research Center in new York,
Almaden in California, Zurich, Haifa and Tokyo, amongst others. The team
first pulled together by Andrea Califano and Barry Robson runs itself
on a panel basis and the panel meets regularly, at New York or by telephone
conference. Each team emphasizes different aspects of the problem: particle
and molecular mechanics simulation, mathematical optimization, the
structure and searching of phase space, force fields, quantum mechanics,
heuristic use of experimental and genome data, pattern recognition and
biological data mining, game theory and computational theory including
parallel processing methods, development of automated protein modeling and
drug design pipelines, and other pharmaceutical, medical and health care
applications including the longer term vision of fast-responce,
personalized molecular medicine.
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