ANNOUNCE ProAnalyst -- new software for protein/peptide analysis

Alexy Eroshkin eroshkin at vector.nsk.su
Mon Sep 9 05:54:23 EST 1996


To: mol-evol at dl.ac.uk
From: eroshkin at vector.nsk.su <Alexey Eroshkin>
Subject: ANNOUNCE ProAnalyst - new software for protein/peptide analysis


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           ProAnalyst - PROTEIN ANALYST (ver 1.02)
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     State Research Center of Virology and Biotechnology
         Koltsovo, Novosibirsk Region, 633159 Russia
                           and
          Vladimir Ivanisenko with Alexey Eroshkin

are pleased to announce the availability of an easy-to-use,
state-of-the-art MS-DOS application designed to solve traditional
and new tasks of protein science.

ProAnalyst FEATURES:

- includes intuitive user interface to facilitate data analysis;
- inputs single and multiple protein sequences, activity/property/
  genotype data, protein 3D structures;
- relates experimental data to protein primary and tertiary structure;
- finds sites influencing protein activity/property;
- finds relationships between protein sites' characteristics
  (hydrophobicity, amphipathicity, etc.) and protein activities;
- investigates differences between proteins divided by functional,
  evolutionary or other criteria (for example, relates genotype
  to phenotype);
- investigates physico-chemical factors related with activity changes in
  a set of mutant proteins (including multiple physico-chemical factors);
- simulates protein-engineering experiments and predicts activity of
  mutant protein;
- searches motifs and patterns in combinatorial libraries (peptide and
  phage-displayed libraries);
- provides linear correlation and multiple linear regression
  analysis, discriminant, ANOVA and alphabetical analysis;
- classic profile/plot analysis for a single sequence (hydrophobicity,
  helical amphipathicity, etc.) suplemented with average, min, max and
  dispresion plots for a set of sequences;
- searches regions with high and low variability of physico-chemical
  characteristics;
- calculates structure-activity correlation profile;
- performs cross and inter-group variability analysis based on
  several matrices of amino acid similarity;
- main part of methods works with sequential and spatial sites;
- maps obtained results onto 3D structure;
- sorts sequences by activity, group number, motifs found;
- visualizes multiple alignments and protein 3D structures (stereo)
  with sites highlighted;
- has data converter from several protein sequence formats (FASTA,
  SWISS-PROT, CLUSTAL, PIR, IG);
- has data bases with 50 aligned protein families, more than 60 amino
  acid properties, HELP, Manual and examples with program applications.

ProAnalyst MAY BE USEFUL:

- for chemists and biochemists making investigations of
  protein structure-function and structure-activity analysis;
- for protein engineers trying to improve some protein properties;
- for molecular biologists that need to get sense from multiple protein
  alignments and to analyze complicated combinatorial libraries;
- for geneticists studying phenotype-genotype correlations;
- for those who need color protein 3D pictures with sites highlighted;
- for students in any field of PROTEIN SCIENCE;
- for those who interested in comparative protein sequence analysis.

PUBLICATIONS:

1. Eroshkin A.M., Zhilkin P.A., Fomin V.I. Algorithm and computer program
PROANAL for analysis of relationship between structure and activity in a
family of proteins or peptides. CABIOS, 1993, 9, 491-497.
2. Eroshkin A.M., Minenkova O.O., Fomin V.A., Ivanisenko V.A., Ilyichev
A.A.  Analysis of peptide fragment insertions into major coat protein of
bacteriophages M13, f1 and fd. Relation of protein structural
characteristics and viability of mutant phages. Molec. Biology (Russia),
1993, 27, 1345-1355.
3. Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.A., Kondrakhin
Y.V.  PROANAL version 2: multifunctional program for analysis of multiple
protein sequence alignments and studying structure-activity relationships
in protein families. CABIOS, 1995, 11, 39-44.
4. Kuzmicheva G.A., Kuvshinov V.N., Razumov I.A., Ivanisenko V.A.,
Eroshkin A.M., et al. Mapping of group specific hemagglutinating
antigenic epitope of alphavirus envelope protein E2 using phage display.
Doklady Academii Nauk RAN, in press.
5. Morozov B.M., Ivanisenko V.A., Eroshkin A.M., Ugarova N.N. Analysis
of relations between bioluminescence color and the structure of beetle
luciferases: identification of the sites influencing bioluminescence
color. Molec. Biology (Russia), in press.

AVAILABILITY:

ProAnalyst is available from EBI software library:
ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst/
(as self-extracted archive).

Current version works with up to 15 sequences. The length of sequences
must be less than or equal to 5000.

Comments, bug reports, suggestions for new features are welcome
and should be sent by e-mail to:
salex at vector.nsk.su (Vladimir Ivanisenko) or
eroshkin at vector.nsk.su (Alexey Eroshkin)

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Alexey Eroshkin               Institute of Molecular Biology
E.mail: eroshkin at vector.nsk.su    State Research Center of Virology and
Tel: +7 (3832) - 647774           Biotechnology "Vector"
Fax: +7 (3832) - 328831           Koltsovo, Novosibirsk Region 633159
                                  Russia
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