SPLIT 4.0 SERVER

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, preference functions, hydrophobicity analysis, sequence, protein sequence, amino acid scales, hydrophobicity scales, hydrophobicity plot, biochemistry, biophysics, biocomputing, bioinformatics, scientific computational server, Davor Juretic, Damir Zucic, Ana Jeroncic and Larisa Zoranic.

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 Davor Juretic , professor at the University of Split , Croatia. This server was written by Damir Zucic, at the University of Osijek , Croatia and Viktor Bojovic, University of Split, 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.

Terms of Use

(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 to read the latest terms of use!

Technical Requirements

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 configuration.

Performance

If you wish to test the performance of SPLIT4 with known structures click here

Data Input Form

Please paste or type your sequence (one letter code) in the frame below. Do not submit the nucleotide sequence! You can submit the sequence in a free, case independent format, just don't forget to remove any extra information (like protein name, code etc).

There are three ways to copy and paste the sequence:

(1) Use an editor to read the sequence file, stored locally on your computer, and copy data to browser window.

(2) Use the SWISS-PROT search to retrieve the sequence. You will need an additional browser window , connected to the SWISS-PROT search engine. If you have no intention to combine SPLIT server with SWISS-PROT right now, try it some other time, you will like it.

(3) If you have no sequence and you don't want to search the SWISS-PROT database, use sample sequences . If you just want to test the SPLIT server this is the easiest way to prepare data. If you wish to test the SPLIT server with a single polypeptide of known structure click here

Membrane protein sequence is the minimal input required by the prediction program. Do not submit the nucleotide sequence!

Type the name of your protein in the small frame below. This input is not required for prediction, so you can ignore it.

Your personal or institutions home page; not required, but we would be pleased if you invite us to visit your pages.

If you allready have both your sequence and your prediction where should be the sequence location of transmembrane helices we can offer nice comparision of SPLIT prediction and your own prediction. To perform such comparision click here

If you want to see the SPLIT4 server usage statistics click here

If you specified the sequence, you can press the submit button to start the prediction.

Technical Notes

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 Linux (more accurately called GNU /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 GNU C compiler (Free Software Foundation) , version 2.7.2.3. 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.

Contact us!

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:

juretic@mapmf.pmfst.hr	zucic@garlic.mefos.hr	alucin@mapmf.pmfst.hr	larisaz@mapmf.pmfst.hr	ezop@judita.pmfst.hr
Davor Juretic Physics Department Faculty of Natural Sciences, Mathematics and Education University of Split Teslina 12 21000 Split Croatia Europe	Damir Zucic School of Medicine University of Osijek Hutlerova 4 31000 Osijek Croatia Europe	Ana Jeroncic Physics Department Faculty of Natural Sciences, Mathematics and Education University of Split Teslina 12 21000 Split Croatia Europe	Larisa Zoranic Physics Department Faculty of Natural Sciences, Mathematics and Education University of Split Teslina 12 21000 Split Croatia Europe	Viktor Bojovic System administrator

Related Web Servers

We have a list of other web servers for membrane protein secondary structure prediction. If you are maintaing the similar server, and are willing to be added to our list, please notify us. Send the short description, with precise address of your server, to Damir Zucic (zucic@garlic.mefos.hr) .

Acknowledgments

This server was partly financed by the Croatian Ministry of Science and Technology. Larisa Zoranic, Ana Jeroncic and Viktor Bojovic provided valuable help during development of this server.

References

Split 4.0 reference:

Juretic, D., Zoranic, L., Zucic, D. "Basic charge clusters and predictions of membrane protein topology"
J. Chem. Inf. Comput. Sci. Vol. 42, pp. 620-632, 2002.

Older references:

1) Juretic, D., Lee, B. K., Trinajstic, N., and Williams, R. W. "Conformational preference functions for predicting helices in membrane proteins."
Biopolymers 33, 255-273 (1993).

2) 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.

3) 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.

4) 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.

5) 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.

6) Juretic, D., Jeroncic, A. and Zucic, D. "Prediction of initiation sites for protein folding." Periodicum Biologorum 101, No 4, 339-347, 1999.