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QCMP139. PROANAL: Multifunctional Program for the Analysis
of Protein Sequences and the Study of the Structure-
Activity Relationship in Protein Families (V. 2.0)
by A. M. Eroshkin, V. I. Fomin and P. A. Zhilkin,
Theoretical Department, Research Institute of Molecular
Biology, SRC VB "Vector", 633159 Koltsovo, Novosibirsk
Region, Russia
PROANAL is an integrated, applied system directed
toward solving many problems in the analysis of the
relationship between structure and activity in a family
of evolutionarily related (and/or artificially mutated)
proteins and peptides. This sytem is based on an
earlier program PRO-ANAL [Eroshkin et al., CABIOS, 9,
491-497 (1993)]and is aimed at providing a
multifunctional analysis of protein sequences (using
the methods of correlation, regression and profile
analysis) and the design of protein engineering
experiments.
This program uses aligned amino acid sequences with
data on their activity (pK, Km, ED50 or any other) and
looks for correlations between activity data and
various physico-chemical characteristics of regions in
primary structures. Physico-chemical characteristics
are calculated using various amino acid factors and
ten different functions for calculation of the
characteristic. These functions include well-known
average values, average alpha-helical moment, beta-
strand moment etc.). In automatic mode, the program
generates and verifies hypotheses on the location of
activity-modulating regions in a protein and on the key
characteristics of these regions. In manual mode, the
user can generate and analyze his own hypotheses.
PROANAL is designed to simulate protein engineering
experiments as well.
Further, the program seeks:
* Protein conserved domains (or functional sites) and
variable regions (or sites for engineering)
* Regions with high or low values of some physico-
chemical characteristics (T- or B-cell antigenic
epitopes, surface regions, transmembrane segments,
etc.).
The search of the first two sites is based on analysis
of dispersion of physico-chemical characteristics in
different proteins along the sequences. The search of
the sites of the last two types is based on the
analysis of mean values of characteristics instead of
dispersions. Using the program you can plot and
analyze the following:
* Structure-activity relationship plots (graph of
linear regression and nonlinear curve fitting)
* Distribution of physico-chemical characteristics
along the sequence, e.g., plot of hydrophilicity, plot
of hydrophobic moments, etc.
* Plots of average of physico-chemical
characteristics along the sequences in the entire set
of aligned amino acid sequences.
The program is implemented for the IBM PC or compatible
computers. It is designed to be handled easily by any
occasional computer user. At the same time, it is
powerful enough for experienced professionals. With
PROANAL one has a multifunctional program which can
satisfy many of one's needs in protein sequence
analysis and design.
Lines of Code: 9911
TURBO C (Borland)
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