profbval_1.0.22-4_all.deb


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Description

profbval - predictor of flexible/rigid protein residues from sequence

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name profbval
Package version 1.0.22
Package release 4
Package architecture all
Package type deb
Installed size 258 B
Download size 57.96 KB
Official Mirror archive.ubuntu.com
PROFbval can be useful for both protein structure and
function predictions. For instance, a biologist can locate potentially
antigenic determinants by identifying the most flexible residues on the
protein surface. Additionally, a crystallographer can locate residues that
potentially have high experimental B-values.
PROFbval takes the following input, further described on profbval(1):
* a protein sequence in a FASTA file
* secondary structure and solvent accessibility prediction by prof(1)
* an HSSP file
Background: the mobility of a given residue on the protein surface is related
to its functional role.
Therefore, identification of extremely rigid or flexible
residues on the protein surface is helpful for identifying functionally
important residues in proteins. A common measure of atom mobility in proteins
is B-value data from x-ray crystallography structures. PROFbval is the first
tool to predict normalized backbone B-values from amino-acid sequence.

Alternatives

Package Version Architecture Repository
profbval_1.0.22-4_all.deb 1.0.22 all Ubuntu Universe
profbval - - -

Requires

Name Value
perl:any -
profnet-bval -

Download

Type URL
Binary Package profbval_1.0.22-4_all.deb
Source Package profbval

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install profbval deb package:
    # sudo apt-get install profbval

Files

Path
/usr/bin/profbval
/usr/share/doc/profbval/README
/usr/share/doc/profbval/README.test
/usr/share/doc/profbval/changelog.Debian.gz
/usr/share/doc/profbval/copyright
/usr/share/doc/profbval/installation-test
/usr/share/doc/profbval/examples/cad23-fil.hssp
/usr/share/doc/profbval/examples/cad23-fil.rdbProf
/usr/share/doc/profbval/examples/cad23.f
/usr/share/doc/profbval/examples/cad23.profbval.gz
/usr/share/man/man1/profbval.1.gz
/usr/share/profbval/nn_files/jct.in
/usr/share/profbval/scr/PROFbval.pl
/usr/share/profbval/scr/createDataFile.pl

Changelog

2016-07-16 - Tatiana Malygina <merlettaia@gmail.com>
profbval (1.0.22-4) unstable; urgency=medium
* Team upload.
* added allow-stderr restriction to debian/tests/control - in case when 
recommended package `pp-popularity-contest` is not installed,
and described that in debian/README.test
* add hardening
2016-06-08 - Tatiana Malygina <merlettaia@gmail.com>
profbval (1.0.22-3) unstable; urgency=medium
* Team upload.
* changed citation in debian/upstream/metadata from search string to 
corresponding PMID article link
* add simple testsuite
* cme fix dpkg-control
* added d/README.test + d/docs, improved installation-test
2016-01-08 - Andreas Tille <tille@debian.org>
profbval (1.0.22-2) unstable; urgency=medium
* Add myself to Uploaders
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* Priority: optional
* debhelper 9
* DEP5 fix
2012-08-14 - Laszlo Kajan <lkajan@rostlab.org>
profbval (1.0.22-1) unstable; urgency=low
* Initial release in Debian (Closes: #680140)
2011-05-16 - Laszlo Kajan <lkajan@rostlab.org>
profbval (1.0.16) unstable; urgency=low
* man page update for multiple output files and formats
* moved references to PP standard section
2011-05-11 - Laszlo Kajan <lkajan@rostlab.org>
profbval (1.0.15) unstable; urgency=low
* Added ability to create multiple outputs with the intention to save
output in multiple formats
2011-01-12 - Laszlo Kajan <lkajan@rostlab.org>
profbval (1.0.14) stable; urgency=low
* Made prof output regexp line recognize more prof outputs
2010-09-20 - Laszlo Kajan <lkajan@rostlab.org>
profbval (1.0.13)
* Input sequence now converted to upper case before processing (and so lower case sequences are now accepted)
2010-06-30 - Laszlo Kajan <lkajan@rostlab.org>
profbval (1.0.12)
* Now accepts `O' as a valid amino acid (for pyrrolysine)
2010-06-29 - Laszlo Kajan <lkajan@rostlab.org>
profbval (1.0.11)
* Now accepts `U' as a valid amino acid (for selenocysteine)

See Also

Package Description
profile-sync-daemon_6.31-1_all.deb Symlink and sync browser profile directories into RAM
profisis_1.0.11-3_all.deb prediction of protein-protein interaction sites from sequence
profitbricks-api-tools_4.1.0-2_all.deb command line tools that use the public API from ProfitBricks
profnet-bval_1.0.22-4build2_i386.deb neural network architecture for profbval
profnet-chop_1.0.22-4build2_i386.deb neural network architecture for profchop
profnet-con_1.0.22-4build2_i386.deb neural network architecture for profcon
profnet-isis_1.0.22-4build2_i386.deb neural network architecture for profisis
profnet-md_1.0.22-4build2_i386.deb neural network architecture for metadisorder
profnet-norsnet_1.0.22-4build2_i386.deb neural network architecture for norsnet
profnet-prof_1.0.22-4build2_i386.deb neural network architecture for profacc
profnet-snapfun_1.0.22-4build2_i386.deb neural network architecture for snapfun
profphd-net_1.0.22-4build2_i386.deb neural network architecture for profphd
profphd-utils_1.0.10-3build1_i386.deb profphd helper utilities convert_seq and filter_hssp
profphd_1.0.42-1_all.deb secondary structure and solvent accessibility predictor
proftmb_1.1.12-6build1_i386.deb per-residue prediction of bacterial transmembrane beta barrels
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