Please read carefully the copyright notice :
J-PBPS: Java - Protein Blocks Prediction Server
Equipe de Bioinformatique Genomique et Moleculaire (EBGM),
INSERM U436, Universite Paris 7 - Denis Diderot,
case 7113, 2 place Jussieu, 75251 PARIS cedex 05
mailto : debrevern@urbb.jussieu.fr, gautier@urbb.jussieu.fr, cathy@urbb.jussieu.fr and hazout@urbb.jussieu.fr
CONTENTS
1. About the method
2. Copyright notice
3. Availability
4. Bug reports and user feedback
5. References
1. About the method
J-PBPS is a program to predict from the sequence local structures
encoded in a structural alphabet called Protein Blocks. The approximation
of 3D structure by the PBs is correct and allows a description closer to
the reality than a simple 3-states alphabet (secondary structures). Then,
the prediction of the local 3D structures from the sequence is done using
a Bayesian approach with a rate of 34.2 %. This rate increases to 40.7 %
by subdividing by an unsupervised method the most frequent PB on their
sequence specificity. The local information is more informative than
expected, 75.8 % of the true PBs are finding again among the fourth most
probable PBs for the Bayesian approach. Please see de Brevern, Etchebest
and Hazout [1] for detailed description of the algorithm.
2. Copyright notice
All rights reserved, whether the whole or part of the program is concerned. Permission to use this software and
its documentation is granted for academic use, provided that:
i. this copyright notice appears in all copies of the software and/or related documentation;
ii. the reference given below (de Brevern et al., 2000) must be
cited in any publication of scientific results based in part or
completely on the use of the program;
iii. bugs will be reported to the authors.
The use of the software in commercial activities is not allowed
without a prior written commercial license agreement (please write to
debrevern@urbb.jussieu.fr and hazout@urbb.jussieu.fr).
WARNING: J-PBPS is provided "as-is" and without warranty of any kind,
express, implied or otherwise, including without limitation any
warranty of merchantability or fitness for a particular purpose. In no
event will the authors be liable for any special, incidental, indirect
or consequential damages of any kind, or any damages whatsoever
resulting from loss of data or profits, whether or not advised of the
possibility of damage, and on any theory of liability, arising out of
or in connection with the use or performance of this software.
3. Availability
J-PBPS is written in Java 2 with jdk 1.3.0 and so could be use with
several UNIX platforms, Windows 95, 98 and 2000, MacOS using IE 4.x
or Netscape 5.x or newer. The prediction site will always be at the
EBGM site (Equipe de Bioinformatique Genomique et Moleculaire) which
is now http://condor.urbb.jussieu.fr. The java bytecode (.class) are
avalaible to academic users for local use from request to
debrevern@urbb.jussieu.fr. The source code (.java) is only avalaible
to commercial users after license agreement.
Due to some limitation of IE and Netscape, the use of the "real" appletviewer
will limit the errors.
4. Bug reports and user feedback
Please send your suggestions, questions and bug reports to debrevern@urbb.jussieu.fr. Send your contact
address to get information on updates and new features.
5. References
de Brevern A.G., Etchebest. C. and Hazout S. (2000) Bayesian probabilistic approach for predicting backbone structures
in terms of protein blocks. Proteins: Structures, Functions and Genetics, 41(3), 271-287.
Does Not Accept Accept.
De BREVERN Alexandre
Equipe de Bioinformatique Genomique & Moleculaire
E03-46 INSERM
Université Paris 7
2, place Jussieu case 7113
75251 Paris Cedex 05
to send a mail
e-mail
with
Subject: Protein Blocks / J-PBPS.