References
- Berman , HM , Westbrook , J , Feng , Z , Gilliland , G , Bhat , TN , Weissig , H , Shindyalov , IN and Bourne , PE . 2000 . The Protein data bank . Nucl. Acids Res. , 28 : 235 – 242 . Database available at http://www.pdb.org/pdb/home/home.do
- Tusnady , GE , Dosztanyi , Z and Simon , I . 2004 . Transmembrane proteins in the protein data bank: Identification and classification . Bioinformatics , 20 : 2964 – 2972 . Database available at http://pdbtm.enzim.hu/
- Chen , CP and Rost , B . 2000 . State-of-the-art in membrane protein prediction . Appl. Bioinformatics , 1 : 121 – 135 .
- Chen , CP , Kernytsky , A and Rost , B . 2002 . Transmembrane helix predictions revisited . Protein Sci. , 11 : 2774 – 2791 .
- Elofsson , A and von Heijne , G . 2007 . Membrane protein structure: Prediction versus reality . Annu. Rev. Biochem. , 76 : 125 – 140 .
- Perl 5.10.1 The Perl Foundation, 2007; Software available at http://www.perl.org/
- Randić , M , Balaban , AT , Novič , M , Založnik , A and Pisanski , T . 2005 . A novel graphical representation of proteins . Period. Biol. , 107 : 403 – 413 .
- Novič , M and Randić , M . 2008 . Representation of proteins as walks in 20-D space . SAR QSAR Environ. Res. , 19 ( 3 ) : 317 – 337 .
- Randić , M , Novič , M and Vračko , M . 2008 . On novel representation of proteins based on amino acid adjacency matrix . SAR QSAR Environ. Res. , 19 : 339 – 349 .
- Wolfenden , R , Andersson , L , Cullis , P and Southgate , C . 1981 . Affinities of amino acid side chains for solvent water . Biochemistry , 20 : 849 – 855 .
- Kyte , J and Doolite , R . 1982 . A simple method for displaying the hydropathic character of a protein . J. Mol Biol. , 157 : 105 – 132 .
- Charton , M and Charton , BI . 1982 . The structural dependence of amino acid hydrophobicity parameters . J. Theor. Biol. , 99 : 629 – 644 .
- Rose , G , Geselowitz , A , Lesser , G , Lee , R and Zehfus , M . 1985 . Hydrophobicity of amino acid residues in globular proteins . Science , 229 : 834 – 838 .
- Hecht-Nielsen , R . 1987 . Counterpropagation networks . Appl. Opt. , 26 : 4979 – 4984 .
- Zupan , J , Novič , M and Ruisanchez , I . 1997 . Kohonen and counterpropagation artificial neural networks in analytical chemistry . Chemom. Int. Lab. Syst. , 38 : 1 – 23 .
- Zupan , J and Gasteiger , J . 1999 . Neural Networks in Chemistry and Drug Designing , 2nd , Weinheim : Wiley-VCH .
- Novič , M and Zupan , J . 1995 . Investigation of infrared spectra-structure correlation using Kohonen and counterpropagation neural network . J. Chem. Inf. Comput. Sci. , 35 : 454 – 466 .
- Tropsha , A , Gramatica , P and Gombar , VK . 2003 . The importance of being earnest: Validation is absolute essential for successful application and interpretation of QSPR models . QSAR Comb. Sci. , 22 : 69 – 77 .
- Gasteiger , J and Zupan , J . 1993 . Neural Networks in chemistry . Angew. Chem. Int. Ed. Engl. , 32 : 503 – 527 .
- Shi , N , Ye , S , Alam , A , Chen , L and Jiang , Y . 2006 . Atomic structure of a Na+- and K+-conducting channel . Nature , 440 : 570 – 574 .
- Battiston , L , Passamonti , S , Macango , A and Sottocasa , GL . 1998 . The bilirubin-binding motif of bilitranslocase and its relation to conserved motifs in ancient biliproteins . Biochem. Biophys. Res. Commun. , 247 ( 3 ) : 687 – 692 .
- Passamonti , S , Terdoslavich , M , Franca , R , Vanzo , A , Tramer , F , Braidot , E , Petrussa , E and Vianello , A . 2009 . Bioavailability of flavonoids: A review of their membrane transport and the function of bilitranslocase in animal and plant organisms . Curr. Drug Metab. , 10 : 369 – 394 .
- Passamonti , S , Terdoslavich , M , Margon , A , Cocolo , A , Medic , N , Macri , F , Decorti , G and Franko , M . 2005 . Uptake of bilirubin into HepG2 cells assayed by thermal lens spectroscopy . FEBS J. , 272 : 5522 – 5535 .
- Passamonti , S , Cocolo , A , Braidot , E , Petrussa , E , Peresson , C , Medic , N , Macri , F and Vianello , A . 2005 . A characterization of electrogenic bromosulfopthalein transport in carnation petal microsomes and its inhibition by antibodies against bilitranslocase . FEBS J. , 272 : 3282 – 3296 .
- Jones , DT , Taylor , WR and Thornton , JM . 1994 . A model recognition approach to the prediction of all-helical membrane protein structure and topology . Biochemistry , 33 : 3038 – 3049 . Available at http://saier-144-37.ucsd.edu/memsat.html
- Tusnády , GE and Simon , I . 1998 . Principles governing amino acid composition of integral membrane proteins: Applications to topology prediction . J. Mol. Biol. , 283 : 489 – 506 . Available at http://www.enzim.hu/hmmtop/html/adv_submit.html
- Rost , B , Yachdav , G and Liu , J . 2004 . The predict protein server . Nucl. Acids Res. , 32 : W321 – W326 . Available at http://www.predictprotein.org/main.php
- Hofmann , K and Stoffel , W . 1993 . Tmbase – A database of membrane spanning proteins segments . Biol. Chem. Hoppe-Seyler , 374 : 166 Available at http://www.ch.embnet.org/software/TMPRED_form.html
- Claros , MG and von Heijne , G . 1994 . TopPred II: An improved software for membrane protein structure predictions . CABIOS , 10 : 685 – 686 . Available at http://mobyle.pasteur.fr/cgi-bin/portal.py?form=toppred
- Yuan , Z , Mattick , JS and Teasdale , RD . 2004 . SVMtm: Support vector machines to predict transmembrane segments . J. Comput. Chem. , 25 ( 5 ) : 632 – 636 . Available at http://ccb.imb.uq.edu.au/svmtm/
- Pashou , EE , Litou , ZI , Liakopoulos , Th.D and Hamodrakas , SJ . 2004 . waveTM: Wavelet-based transmembrane segment prediction . In Silico Biol. , 4 : 0012 Available at http://athina.biol.uoa.gr/bioinformatics/waveTM/
- Kall , L , Krogh , A and Sonnhammer , E . 2004 . A combined transmembrane topology and signal peptide prediction method . J. Mol. Biol. , 338 : 1027 – 1036 . Available at http://phobius.sbc.su.se/
- Reynolds , SM , Kall , L , Riffle , ME , Bilmes , JA and Noble , WS . 2008 . Transmembrane topology and signal prediction using Dynamic Bayesian Networks . PLoS Comput. Biol. , 4 : e1000213 Available at http://www.yeastrc.org/philius/pages/philius/runPhilius.jsp
- University of Athens. A Java-program which combines the results of several methods (available through the Internet) that predict transmembrane regions in proteins in a joint prediction histogram. Available at http://athina.biol.uoa.gr/CoPreTHi/InputTrans.html
- Arai , M , Mitsuke , H , Ikeda , M , Xia , JX , Kikuchi , T , Satake , M and Shimizu , T . 2004 . ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability . Nucl. Acids Res. , 32 : W390 – W393 . Available at http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/
- Piedachu , P , Lopez , D and Campos , M . 2008 . IgTm: An algorithm to predict transmembrane domains and topology in proteins . BMC Bioinfo. , 9 : 367 – 377 . Available at www.dsic.upv.es/users/tlcc/bio/bio.html
- Bagos , PG , Liakopoulos , TD and Hamodrakas , SJ . 2006 . Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins . BMC Bioinfo. , 7 : 189 – 205 . Available at http://bioinformatics.biol.uoa.gr/HMM-TM/input.jsp
- Ganapathiraju , M , Jursa , CJ , Karimi , HA and Klein-Seetharaman , J . 2007 . Tmpro: Transmembrane helix prediction through amino acid property analysis . Bioinfo. Adv. Acc. , Available at http://linzer.blm.cs.cmu.edu/tmpro/