biocomputing laboratory

[Gribskov, Michael]

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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