ProMSED, ProAnWin, ProAnalyst
State Research Center of Virology and Biotechnology "Vector"
Koltsovo, Novosibirsk Region, 633159 Russia
with
Vladimir Ivanisenko, Irina Pika, Anatoly Frolov and Alexey Eroshkin
are pleased to announce the availability of easy-to-use,
state-of-the-art applications designed to solve traditional
and new tasks of protein science:
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ProMSED ver 1.10: Protein Multiple Sequences EDitor for Windows 3.x/95
ProMSED is an easy-to-use application for Windows 3.11/95 that performs
automatic and manual multiple protein sequences alignment, alignment
visualization and editing. The program automatically recognises and
reads NBRF/PIR, Pearson (Fasta), EMBL/SwissProt, Intelligenetics and
CLUSTAL and has interface and the main functions similar to popular text
editor Word. Automati alignment is based on ClustalV algorithm. Manual
alignment and sequence visual analysis are facilitated by using of group
operations and amino acid color-coding reflecting amino acid similarity
in physico-chemical and mutational properties, secondary structure
propensities, etc. Size and number of sequences have no limits others
then those imposed by current computer memory. ProMSED can align
complete set of sequences, its subset and any selected block, providing
thus flexible tool for sequence's analysis, visualization, editing and
illustrations preparation.
ProMSED is available from EBI software library:
ftp://ftp.ebi.ac.uk/pub/software/dos/promsed/
(as self-extracted archive).
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ProAnWin: Protein structure-activity/property analysis and design of
protein engineering experiments (for MS Windows 3.x/95)
o Data input from main protein sequence formats (SWISS-PROT, PIR, FASTA,
GCG, CLUSTAL);
o Databases of more then 50 amino acid physico-chemical properties;
o Reads 3D protein structure in PDB format;
o Flexible input of user-defined protein activities, properties or
related phenotypes;
o Multiple protein sequences alignment (Clustal V algorithm);
o Threading multiple sequence alignment onto known 3-dimensional
structure;
o Searching sites influencing protein activity and analyzing
relationships between protein site structural characteristics and
protein activities (properties or related phenotypes);
o Multiple linear regression analysis of structure-activity
relationships;
o Genotype -- phenotype correlation analysis (e.g., in studying
virus drug resistance);
o Investigation of physico-chemical factors related with activity or
property changes in mutant proteins;
o Flexible visualization of protein 3D structures with sites highlighted;
o Activity, property or phenotype prediction;
o Output of all obtained results into text file.
ProAnWin is available at
iubio.bio.indiana.edu, in directory /molbio/ibmpc/ as paw.exe.
Access to iubio by ftp, http, and gopher methods are supported.
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ProAnalyst: Multifunctional analysis of protein sequences and structures
(MS DOS version of ProAnWin with additional functionality).
o Investigation of structural differences between proteins divided by
functional, evolutionary or other criteria;
o Structure-activity relationships investigation by multiple regression
and discriminant analysis;
o Searching motifs in combinatorial libraries (peptide, phage-display
libraries, etc.) with motif mapping on the target protein;
o Protein-engineering experiments design and activity prediction;
o Intra and cross group variability analysis;
o Sorting sequences by protein activity value, protein group number and
by motifs found;
o Alphabetical and physico-chemical analysis of protein features
variations (in 1D and 3D structures);
o 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;
o Structure-activity determination profile (SAD);
o Mapping all obtained results on 3D structure and sequence;
o Flexible molecular graphics (stereo);
o Data conversion from several protein sequence formats (FASTA,
SWISS-PROT, PIR, CLUSTAL);
o Has data bases with 50 aligned protein families, more than 60 amino
acid properties, HELP, Manual and examples with program applications.
ProAnalyst is available from EBI software library:
ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst/
(as self-extracted archive).
