On behalf of Prof. E.R.P. Zuiderweg and Prof. G. Crippen I am posting
the following announcement:
Dear Colleagues:
Forgive us for sending you this "advertisement". It pertains to the
automatic triple-resonance assignment software called "SAGA", which was
developed by Gordon Crippen and Erik Zuiderweg over the last two years.
It is an enhanced version of the software described in our recent
publication(1).
We truly believe SAGA has solved the NMR protein assignment problem:
(1) Small proteins like the 180-residue protein files included in the
release, are assigned in less than 5 minutes on a laptop computer.
(2) We tested it for proteins up to 750 residues --- correct assignments
are found within an hour on a laptop computer.
(3) We tested it with incomplete real data from proteins of 380 residues
-- assignments AND ALTERNATIVE FEASIBLE ASSIGNMENTS, with a probability
score, are obtained in an hour or so.
(4) Required input data: HN(CO)CA, HNCA and HNCACB.
Optional: HNCO, HN(CA)CO and HN(CO)CACB.
(5) Optional: constraints such as obtained from residue-selective labeling.
(6) Input data is read from NMRPipe or Sparky peak-pick files.
(7) The program is written in Python 2.6, and was tested under MacOS
10.5 and 10.6 on a Intel Macbook Pro and under Red Hat Enterprise Linux
5.5 on a Dell Precision 380 .
* A full-function but time-limited demonstration copy for Mac or Linux
running Python 2.6, together with manual, tutorial, demo data, and
associated license, is attached to this message. Use of this evaluation
version constitutes acceptance of the attached license. This evaluation
version will expire in September of this year. We request that you will
quote our paper below if the program yields results that end up in a
publication.
Fully licensed non-expiring versions of the program can be downloaded
from
http://www.ibridgenetwork.org/umich/saga-software-for-assignment-of-nmr-spectra-of-proteins.
The license is free of charge for academics and not-for profit
organizations.
I really hope you will try SAGA - and have your students and post-docs
spend their time doing science instead of solving puzzles.
Sincerely,
Erik Zuiderweg and Gordon Crippen.
(1) SAGA: rapid automatic mainchain NMR assignment for large proteins.
<
http://www.ncbi.nlm.nih.gov/pubmed/20232231>
Crippen GM, Rousaki A, Revington M, Zhang Y, Zuiderweg ERP.
J Biomol NMR 46, 281-298 (2010)
* As attachments are not welcome in this network, please send your requests.
--
_____________________________
Alex V. Kurochkin, Ph.D.
Research Specialist Lead
The University of Michigan
College of Literature, Science& Arts
Phone: 734-763-0329
Fax: 734-764-3323
E-mail:akur_at_umich.edu
Received on Fri Aug 27 2010 - 10:18:45 MST