Dr. Curtiss:
This may be at somewhat of a tangent to your request for information from
existing biocomputing facilities since I am not currently a part of such a
facility, however I though I would send my comments, for whatever they
are worth. It wasn't comepletely clear to me from your posting whether
you are proposing a biocomputing lab that would be oriented towards
providing a service using existing techniques, or to basic research in
biocomputing. My impression is that you meant a research facility that
would also have a strong service component.
There are a number of facilities that meet this description such as
NCBI (Lipman), EMBL (Argos), MBCRR (Smith), NCI-Laboratory of Math. Biol.
(Maizel), NCI-Advanced Scientific Computing Lab (NCI Supercomputer
facility), and probably many others. There are as well many more
service oriented facilities. I think that you are probably well aware
of the sites I listed above so I will not bother to include addresses.
My interests can be succinctly described as computational molecular
biology. I think a biocomputing facility could be an enormous help to
biological researchers in providing expertise and assistance on the
following topics, since most molecular biologists do not have the time
to become expert in these (for them) peripheral areas.
protein structure prediction
secondary structure
homology based modeling
structure comparison and definition of structural motifs
superposition of multiple structures
inference of sequence characteristics from structure
recognition of sequence patterns typical of structural motifs
definition of fundamental structural elements
sequence comparison and definition of sequence motifs
sequence alignment
multiple sequence alignment
inference of patterns from aligned sequences
recognition of sequence patterns
protein motifs
DNA/RNA signals (promoters,terminators,splice signals)
database screening for patterns
molecular dynamics
RNA folding
phylogenetic analysis
Database development/management
(crystallographic and NMR determination of structures)
Not to seem pushy, but since I am currently looking for a position, I
would be very interested to know if your plans include the possibility
of faculty level positions involved with the biocomputing lab. I have
5 years of post graduate experience in the areas of proteins structure
and protein and nucleic acid sequence analysis and would be very interested
in such a position. My main interests are in methods to define and
identify protein structural and sequence motifs, in the constraints that
structure and function place on the evolution of proteins, and in the
analysis of genomic sequence data. I would be happy to send a cv if you are
interested.
Michael Gribskov
Scientist Associate
NCI-FCRDC
gribskov at ncifcrf.gov
(301) 846-5031
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