Software for sequence/structure matching?

Konrad, IRBM Chemistry, +39-6-91093606 koehler at irbm.it
Sun Sep 19 21:32:00 EST 1993


     As a follow-up to Simon Brocklehurst's message about sequence/structure
comparisons, I have an additional (and perhaps mundane) question:

     Are there any publicly available software packages to perform these sorts
of analyses?  I have heard that Eisenberg's method is available through Biosym
and Blundell's stuff through Tripos but both of these options are rather pricey.
We are looking for a low cost option.

     We are attempting to homology model a protein which has low (>10%) sequence
homology to any structure available in the Brookhaven database.  We have tried
all the standard "2D" alignment methods between our sequence and the sequences
for which 3D structure is available and the alignment for much of the sequence
remains uncertain.   Therefore would like to try some of the 3D threading
methods.

     Please respond directly to me and if there are sufficient responses, I will
summarize and post to the net.

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Konrad Koehler              |  Computational Chemistry Group     |
internet:  koehler at irbm.it  |  Department of Medicinal Chemistry |
                            |  IRBM                              |
telephone: +39-6-910-93606  |  Via Pontina Km 30.600             |
fax:       +39-6-910-93225  |  00040 Pomezia (Roma)              |
                            |  Italy                             |
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