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Package: wnpp
Severity: wishlist
Owner: Laszlo Kajan <lkajan@rostlab.org>
* Package name : profphd
Version : 1.0.35
Upstream Author : Laszlo Kajan <lkajan@rostlab.org>
* URL : http://rostlab.org/
* License : GPL
Programming Lang: Perl
Description : secondary structure and solvent accessibility predictor
Solvent accessibility is predicted by a neural network method rating at a
correlation coefficient (correlation between experimentally observed and
predicted relative solvent accessibility) of 0.54 cross-validated on a set of
238 globular proteins (Rost & Sander, Proteins, 1994, 20, 216-226;
evaluation of accuracy). The output of the neural network codes for 10 states
of relative accessibility. Expressed in units of the difference between
prediction by homology modelling (best method) and prediction at random
(worst method), PROFacc is some 26 percentage points superior to a comparable
neural network using three output states (buried, intermediate, exposed) and
using no information from multiple alignments.
.
Transmembrane helices
in integral membrane proteins are predicted by a system of neural networks.
The shortcoming of the network system is that often too long helices are
predicted. These are cut by an empirical filter. The final prediction
(Rost et al., Protein Science, 1995, 4, 521-533; evaluation of accuracy)
has an expected per-residue accuracy of about 95%. The number of false
positives, i.e., transmembrane helices predicted in globular proteins, is
about 2%.
.
The neural network prediction of transmembrane helices
(PHDhtm) is refined by a dynamic programming-like algorithm. This method
resulted in correct predictions of all transmembrane helices for 89% of the
131 proteins used in a cross-validation test; more than 98% of the
transmembrane helices were correctly predicted. The output of this method
is used to predict topology, i.e., the orientation of the N-term with respect
to the membrane. The expected accuracy of the topology prediction is > 86%.
Prediction accuracy is higher than average for eukaryotic proteins and lower
than average for prokaryotes. PHDtopology is more accurate than all other
methods tested on identical data sets.
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--- Begin Message ---
Source: profphd
Source-Version: 1.0.37-1
We believe that the bug you reported is fixed in the latest version of
profphd, which is due to be installed in the Debian FTP archive:
profphd_1.0.37-1.debian.tar.gz
to main/p/profphd/profphd_1.0.37-1.debian.tar.gz
profphd_1.0.37-1.dsc
to main/p/profphd/profphd_1.0.37-1.dsc
profphd_1.0.37-1_all.deb
to main/p/profphd/profphd_1.0.37-1_all.deb
profphd_1.0.37.orig.tar.gz
to main/p/profphd/profphd_1.0.37.orig.tar.gz
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 643324@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Laszlo Kajan <lkajan@rostlab.org> (supplier of updated profphd package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Wed, 28 Sep 2011 14:51:19 +0200
Source: profphd
Binary: profphd
Architecture: source all
Version: 1.0.37-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Laszlo Kajan <lkajan@rostlab.org>
Description:
profphd - secondary structure and solvent accessibility predictor
Closes: 643324
Changes:
profphd (1.0.37-1) unstable; urgency=low
.
* Initial release in Debian (Closes: #643324)
* New upstream release
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