Membrane Protein Secondary Structure Prediction Server
Transmembrane, transmembrane structure, protein transmembrane structure,
transmembrane structure prediction, protein transmembrane structure prediction,
membrane protein structure, structure prediction,
protein structure prediction, protein secondary structure,
protein secondary structure prediction, membrane protein structure prediction,
membrane protein secondary structure prediction,
hydrophobicity analysis, sequence, protein sequence, amino acid scales,
hydrophobicity scales, hydrophobicity plot, biochemistry, biophysics,
biocomputing, scientific computational server,
Davor Juretic, Damir Zucic, Ana Jeroncic.
The purpose of this server is to predict the transmembrane (TM) secondary
structures of membrane proteins, using the method of preference functions.
Scientific publications describing the method are listed at the bottom of
this page. The method was invented by
, professor at the
University of Split
, Croatia. This server was written by
University of Osijek
, Croatia. See the page bottom for technical details about the server.
Ana Jeroncic was involved both in development of the prediction program and
in testing of this server.
(1) Academic, educational and any other noncommercial use of this software
is free of charge.
(2) Commercial use of this software has to be negotiated with
the project leader,
prof. dr. Davor Juretic
(see the address at the page bottom), except for the trial period of
two days. The trial period is counted per site, not per user.
(3) Every access to this server is logged. If you don't like this,
please disconnect now.
(4) The authors retain the right to change the licensing policy. Be sure
Your browser may be connected to the Internet through a proxy server.
If this is the case, you will be unable to retrieve the correct prediction
results. Change the configuration of your browser to avoid this problem.
This should be very easy; if you don't know how to switch off the proxy
server, ask your local administrator or any person familiar with browser
The prediction program was written in FORTRAN 77. The rest of the server
was written in HTML, version 3 (this form, for example, and all other HTML
documents), ANSI C (output data conversion and graphics) and unix shell
script language (CGI script).
Most of development was done on personal computers running
(more accurately called
/Linux) operating system. FORTRAN to C translator (D. Gay, S. Feldman,
M. Maimone and N. Schryer, copyright AT&T Bell Laboratories and Bellcore)
was used to translate the FORTRAN code. C sources were compiled using
(Free Software Foundation)
, version 184.108.40.206.
Almost all parts of this server are portable across different unix and unix
compatible platforms. The graphics library can be used to plot other types
of scientific data.
This instance of the server is installed on GNU/Linux computer splitbioinf.pmfst.hr.
We have long-term plans to further develop both our prediction method and
this server. Any feedback about your experience with SPLIT server will be
of great value for us. We are open for your criticism, suggestions,
comments and questions. Feel free to contact us at:
This server was partly financed by the Croatian Ministry of Science
and Technology. Igor Susenka and Ivica Loncar, system administrators at
the Faculty of Electrotechnics, University of Osijek, provided valuable
help during development of this server.
Juretic, D., Lee, B. K., Trinajstic, N., and Williams, R. W.
"Conformational preference functions for predicting helices in
Biopolymers 33, 255-273 (1993).
1) Juretic, D., Lucic, B., Zucic, D. and Trinajstic, N.
"Protein transmembrane structure: recognition and prediction
by using hydrophobicity scales through preference functions."
Theoretical and Computational Chemistry, Vol.5. Theoretical
Organic Chemistry, pp. 405-445. Editor: Parkanyi, C.,
Elsevier Science, Amsterdam, 1998.
SPLIT 3.1 results are described in that paper.
2) Juretic, D., Zucic, D., Lucic, B. and Trinajstic, N.
"Preference functions for prediction of membrane-buried helices
in integral membrane proteins."
Computers Chem. Vol. 22, No. 4, pp. 279-294, 1998.
SPLIT 3.1 results are described in that paper as well.
3) Juretic, D. and Lucin A. "The preference functions method for
predicting protein helical turns with membrane propensity."
J. Chem. Inf. Comput. Sci. Vol. 38, No. 4, pp. 575-585, 1998.
SPLIT 3.5 results are described in that paper.
4) Juretic, D., Jeroncic, A. and Zucic, D.
"Sequence analysis of membrane proteins with the web server SPLIT."
Croatica Chemica Acta Vol. 72, No. 4, pp. 975-997, 1999.
5) Juretic, D., Jeroncic, A. and Zucic, D.
"Prediction of initiation sites for protein folding."
Periodicum Biologorum 101, No 4, 339-347, 1999.