ANNOUCING PRANA - NEW PROTEIN STRUCTURE-ACTIVITY ANALYSIS SOFTWARE

Alexy Eroshkin eroshkin at vector.nsk.su
Fri Feb 9 23:16:29 EST 1996


To:  bionews at dl.ac.uk
From:  eroshkin at vector.nsk.su <Alexey Eroshkin>
Subject: ANNOUNCING PRANA - NEW PROTEIN STRUCTURE-ACTIVITY ANALYSIS SOFTWARE


-------------------------------------------------------------------
 PRANA : PC-based program for studying the relationships between
     structure and activity in protein/peptide families
-------------------------------------------------------------------
                         by
          I.Pika, V.Ivanisenko & A.Eroshkin

State Research Center of Virology and Biotechnology "Vector" Koltsovo,
           Novosibirsk Region, 633159 Russia

    E.mail: eroshkin at vector.nsk.su, Tel: +7 (3832) - 647774,
                Fax: +7 (3832) - 328831
-------------------------------------------------------------------

The State Research Center of Virology and Biotechnology "VECTOR" is
pleased to announce the availability of PRANA v1.0.
PRANA is an easy-to-use, state-of-the-art MSDOS application for studying
the relationships between structure and activity in protein/peptide
families divided in two groups (by activity, property, evolution, etc.).
The program examines the relationships between protein grouping and
physico-chemical characteristics (e.g., mean Hydrophobicity, Charge, or
Volume, alpha-helical or beta-strand moments of Hydrophobicity, etc.) of
different regions in their primary structures and delineates the sites
and characteristics describing the given grouping.

PRANA is based on the program PROANAL (A. Eroshkin, V.Fomin, P.Zhilkin,
CABIOS, 1993, 9, 491-497) and designed to provide analysis of additional
data. PROANAL looks for correlations between quantitative data on
protein activity and physico-chemical characteristics of the regions in
the primary structures. In case of PRANA the analysis is based on
aligned amino acid sequences and data on protein grouping (qualitative
activity data). The program searches activity-modulating regions in
aligned proteins that have different structure characteristics for two
groups (biophore or pharmacophore).  Student's or Kolmogorov - Smirnov's
criteria are used to compare the distributions of the characteristics in
two protein groups. The results - found sites and their physico-chemical
characteristics as well as all necessary statistical evaluations - are
presented in the form of text and histograms that can be saved or
printed as required.

PRANA CAN BE USED:

- to find sites and site characteristics that may be responsible for
the difference in proteins activity or property;

- to classify newly sequenced proteins/peptides;

- to assist in simulation of protein engineering experiments.

EXAMPLES OF DATA TYPES TO BE ANALYZED

- 15 variants of human alpha-interferons can be divided into two groups
of high and low antiviral activity. The task is to find amino
acid residues in IFN-alpha related with this difference in activity;

- influenza A virus M(2) proteins from virus strain resistant or
sensitive to amantadine. The task: to find amino acid residues in M(2)
involved in amantadine binding and amino acid physico-chemical
properties important for this interaction.

- peptides inserted into VP1 protein of poliovirus type 1.  Some of
mutant viruses were viable, other - not. The task: to find the
physico-chemical characteristics of the peptide inserts, that are
important for mutant virus viability.


PRANA HAS

* converter from SWISS-PROT, CLUSTAL, GCG, PHYLIP formats to PRANA
  input files;
* data files with about 100 amino acid physico-chemical properties;
* examples, manual and help system.

REQUIREMENTS: DOS 3.30 or later, EGA/VGA video card, 400 KB RAM.

PRANA AVAILABILITY

PRANA v1.0 is freely available for academic users through EBI ftp
server ftp.ebi.ac.uk  (directory  /pub/software/dos/prana).
For companies inquire to:

Alexey Eroshkin
SRC VB "Vector"
Koltsovo, Novosibirsk Region
633159 Russia
E.mail: eroshkin at vector.nsk.su
Tel: +7 (3832) - 647774
Fax: +7 (3832) - 328831


PRANA USERS

Don't hesitate to contact us in case of problems, bugs or suggestions.
Could you send us your address (Email is preferred) and your feelings about
your PRANA experience?




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