A WORKBENCH FOR COMPUTATIONAL
ANALYSIS OF PROTEIN SEQUENCE
AND STRUCTURE ON THE INTERNET
Liakopoulos, Th.D., Palaios, G.A., Probonas, V.I.,
Hamodrakas, J.S., Pasquier, C.M. and Hamodrakas, S.J.
Department of Cell Biology and Biophysics,
Faculty of Biology, University of Athens, Athens 15701
Computational analysis of protein sequences with statistical models, machine
learning techniques or empirical rules leads to prediction of structural and
functional features of the corresponding molecules. Taking into account the
recent explosion of biological information in terms of complete genome
sequences the use of computational tools of analysis is considered essential.
Individual tools are available through the Internet, and their performance
depends on their liability and simplicity of use. We present a workspace that
establishes data trafficking towards a collection of tools (developed also by
our team), communication between them and simple representation of the results
of sequence and structure analysis. At the sequence level, the following are
now offered: Analysis of periodical features, structural classification with
neural networks, prediction of secondary structure, prediction and topology of
transmembrane regions and multiple sequence alignment. At the structure level,
the creation and representation of protein structures and three-dimensional fit
is possible. The end-user is offered with a user-friendly interface and a
simple representation of the results. The system's open and decentralized
design permits the addition of new individual modules that may reside anywhere
on the Internet. Our future plans include the development of modules for fold
recognition, receptor prediction and sequence complexity analysis.
Interconnection between the system, the individual tools and the user is
established through the HTTP protocol, the only requirement for its usage being
Internet access.
Greek
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