Skip to main content

Advertisement

SpringerLink
Log in

Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity

  • Published:
Amino Acids Aims and scope Submit manuscript

Summary.

Transmembrane (TM) proteins represent about 20–30% of the protein sequences in higher eukaryotes, playing important roles across a range of cellular functions. Moreover, knowledge about topology of these proteins often provides crucial hints toward their function. Due to the difficulties in experimental structure determinations of TM protein, theoretical prediction methods are highly preferred in identifying the topology of newly found ones according to their primary sequences, useful in both basic research and drug discovery. In this paper, based on the concept of pseudo amino acid composition (PseAA) that can incorporate sequence-order information of a protein sequence so as to remarkably enhance the power of discrete models (Chou, K. C., Proteins: Structure, Function, and Genetics, 2001, 43: 246–255), cellular automata and Lempel-Ziv complexity are introduced to predict the TM regions of integral membrane proteins including both α-helical and β-barrel membrane proteins, validated by jackknife test. The result thus obtained is quite promising, which indicates that the current approach might be a quite potential high throughput tool in the post-genomic era. The source code and dataset are available for academic users at liml@scu.edu.cn.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • PG Bagos TD Liakopoulos IC Spyropoulas SJ Hamodrakas (2004) ArticleTitlePRED-TMBB: a web server for predicting the topology of β-barrel outer membrane proteins Nucleic Acids Res 32 W400–W404 Occurrence Handle15215419 Occurrence Handle10.1093/nar/gkh417 Occurrence Handle1:CAS:528:DC%2BD2cXlvFKnurs%3D

    Article  PubMed  CAS  Google Scholar 

  • YD Cai KC Chou (2004a) ArticleTitlePredicting 22 protein localizations in budding yeast Biochem Biophys Res Commun 323 425–428 Occurrence Handle10.1016/j.bbrc.2004.08.113 Occurrence Handle1:CAS:528:DC%2BD2cXnsVyqtr4%3D

    Article  CAS  Google Scholar 

  • YD Cai KC Chou (2004b) ArticleTitlePredicting subcellular localization of proteins in a hybridization space Bioinformatics 20 1151–1156 Occurrence Handle10.1093/bioinformatics/bth054 Occurrence Handle1:CAS:528:DC%2BD2cXjs1Wrt78%3D

    Article  CAS  Google Scholar 

  • YD Cai GP Zhou KC Chou (2005) ArticleTitlePredicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition J Theor Biol 234 145–149 Occurrence Handle15721043 Occurrence Handle10.1016/j.jtbi.2004.11.017 Occurrence Handle1:CAS:528:DC%2BD2MXhtlOkt74%3D

    Article  PubMed  CAS  Google Scholar 

  • BQ Cao A Porollo R Adamczak M Jarrell J Meller (2006) ArticleTitleEnhanced recognition of protein transmembrane domains with prediction-based structural profiles Bioinformatics 22 303–309 Occurrence Handle16293670 Occurrence Handle10.1093/bioinformatics/bti784 Occurrence Handle1:CAS:528:DC%2BD28XhtFais74%3D

    Article  PubMed  CAS  Google Scholar 

  • CP Chen B Rost (2002) ArticleTitleState-of-the-art in membrane protein prediction Applied Bioinformatics 1 21–35 Occurrence Handle15130854 Occurrence Handle1:CAS:528:DC%2BD3sXotVers78%3D

    PubMed  CAS  Google Scholar 

  • C Chen Y Tian X Zou P Cai (2006a) ArticleTitleUsing pseudo-amino acid composition and support vector machine to predict protein structural class J Theor Biol 243 444–448 Occurrence Handle10.1016/j.jtbi.2006.06.025 Occurrence Handle1:CAS:528:DC%2BD28XhtFKlsL3N

    Article  CAS  Google Scholar 

  • C Chen X Zhou Y Tian X Zou P Cai (2006b) ArticleTitlePredicting protein structural class with pseudo-amino acid composition and support vector machine fusion network Anal Biochem 357 116–121 Occurrence Handle10.1016/j.ab.2006.07.022 Occurrence Handle1:CAS:528:DC%2BD28XpsVOgs78%3D

    Article  CAS  Google Scholar 

  • KC Chou L Carlacci GM Maggiora (1990) ArticleTitleConformational and geometrical properties of idealized beta-barrels in proteins J Mol Biol 213 315–326 Occurrence Handle2342109 Occurrence Handle10.1016/S0022-2836(05)80193-7 Occurrence Handle1:CAS:528:DyaK3cXkslehurg%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou CT Zhang (1994) ArticleTitlePredicting protein folding types by distance functions that make allowances for amino acid interactions J Biol Chem 269 22014–22020 Occurrence Handle8071322 Occurrence Handle1:CAS:528:DyaK2cXlslCls7o%3D

    PubMed  CAS  Google Scholar 

  • KC Chou CT Zhang (1995) ArticleTitleReview: prediction of protein structural classes Crit Rev Biochem Mol Biol 30 275–349 Occurrence Handle7587280 Occurrence Handle10.3109/10409239509083488 Occurrence Handle1:CAS:528:DyaK2MXosFentb8%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou (1995) ArticleTitleA novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space Proteins Struct Funct Genet 21 319–344 Occurrence Handle7567954 Occurrence Handle10.1002/prot.340210406 Occurrence Handle1:CAS:528:DyaK2MXls12rsb0%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou W Liu GM Maggiora CT Zhang (1998) ArticleTitlePrediction and classification of domain structural classes Proteins Struct Funct Genet 31 97–103 Occurrence Handle9552161 Occurrence Handle10.1002/(SICI)1097-0134(19980401)31:1<97::AID-PROT8>3.0.CO;2-E Occurrence Handle1:CAS:528:DyaK1cXit1yms70%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou DW Elrod (1999) ArticleTitleProtein subcellular location prediction Protein Eng 12 107–118 Occurrence Handle10195282 Occurrence Handle10.1093/protein/12.2.107 Occurrence Handle1:CAS:528:DyaK1MXhvFehs7g%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou (2000a) ArticleTitlePrediction of protein subcellular locations by incorporating quasi-sequence-order effect Biochem Biophys Res Commun 278 477–483 Occurrence Handle10.1006/bbrc.2000.3815 Occurrence Handle1:CAS:528:DC%2BD3cXotlKksbs%3D

    Article  CAS  Google Scholar 

  • KC Chou (2000b) ArticleTitleReview: prediction of protein structural classes and subcellular locations Curr Protein Pept Sci 1 171–208 Occurrence Handle10.2174/1389203003381379 Occurrence Handle1:CAS:528:DC%2BD3cXnsVeisL0%3D

    Article  CAS  Google Scholar 

  • KC Chou (2000c) ArticleTitleReview: prediction of tight turns and their types in proteins Anal Biochem 286 1–16 Occurrence Handle10.1006/abio.2000.4757 Occurrence Handle1:CAS:528:DC%2BD3cXntlKrsL0%3D

    Article  CAS  Google Scholar 

  • KC Chou (2001) ArticleTitlePrediction of protein cellular attributes using pseudo amino acid composition Proteins Struct Funct Genet 43 246–255 Occurrence Handle11288174 Occurrence Handle10.1002/prot.1035 Occurrence Handle1:CAS:528:DC%2BD3MXjtFOls74%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou YD Cai (2002) ArticleTitleUsing functional domain composition and support vector machines for prediction of protein subcellular location J Biol Chem 277 45765–45769 Occurrence Handle12186861 Occurrence Handle10.1074/jbc.M204161200 Occurrence Handle1:CAS:528:DC%2BD38XovFKjurg%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou YD Cai (2003a) ArticleTitlePredicting protein quaternary structure by pseudo amino acid composition Proteins Struct Funct Genet 53 282–289 Occurrence Handle10.1002/prot.10500 Occurrence Handle1:CAS:528:DC%2BD3sXotVSqurk%3D

    Article  CAS  Google Scholar 

  • KC Chou YD Cai (2003b) ArticleTitlePrediction and classification of protein subcellular location: sequence-order effect and pseudo amino acid composition J Cell Biochem 90 1250–1260 Occurrence Handle10.1002/jcb.10719 Occurrence Handle1:CAS:528:DC%2BD3sXpslSgsb4%3D

    Article  CAS  Google Scholar 

  • KC Chou YD Cai (2004a) ArticleTitlePredicting protein structural class by functional domain composition Biochem Biophys Res Commun 321 1007–1009 Occurrence Handle10.1016/j.bbrc.2004.07.059 Occurrence Handle1:CAS:528:DC%2BD2cXmt1Ogtb0%3D

    Article  CAS  Google Scholar 

  • KC Chou YD Cai (2004b) ArticleTitlePredicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition J Cell Biochem 91 1197–1203 Occurrence Handle10.1002/jcb.10790 Occurrence Handle1:CAS:528:DC%2BD2cXjt1yntrY%3D

    Article  CAS  Google Scholar 

  • KC Chou YD Cai (2004c) ArticleTitlePrediction of protein subcellular locations by GO-FunD-PseAA predictor Biochem Biophys Res Commun 320 1236–1239 Occurrence Handle10.1016/j.bbrc.2004.06.073 Occurrence Handle1:CAS:528:DC%2BD2cXls1eisL0%3D

    Article  CAS  Google Scholar 

  • KC Chou YD Cai (2005) ArticleTitlePredicting protein localization in budding yeast Bioinformatics 21 944–950 Occurrence Handle15513989 Occurrence Handle10.1093/bioinformatics/bti104 Occurrence Handle1:CAS:528:DC%2BD2MXis1Oquro%3D

    Article  PubMed  CAS  Google Scholar 

  • KC Chou (2005a) ArticleTitleUsing amphiphilic pseudo amino acid composition to predict enzyme subfamily classes Bioinformatics 21 10–19 Occurrence Handle10.1093/bioinformatics/bth466 Occurrence Handle1:CAS:528:DC%2BD2MXisVWitw%3D%3D

    Article  CAS  Google Scholar 

  • KC Chou (2005b) ArticleTitlePrediction of G-protein-coupled receptor classes J Proteome Res 4 1413–1418 Occurrence Handle10.1021/pr050087t Occurrence Handle1:CAS:528:DC%2BD2MXks1Kgsb4%3D

    Article  CAS  Google Scholar 

  • KC Chou HB Shen (2006a) ArticleTitlePredicting protein subcellular location by fusing multiple classifiers J Cell Biochem 99 517–527 Occurrence Handle10.1002/jcb.20879 Occurrence Handle1:CAS:528:DC%2BD28XhtVSktL3J

    Article  CAS  Google Scholar 

  • KC Chou HB Shen (2006b) ArticleTitleHum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization Biochem Biophys Res Commun 347 150–157 Occurrence Handle10.1016/j.bbrc.2006.06.059 Occurrence Handle1:CAS:528:DC%2BD28Xmslyrsbc%3D

    Article  CAS  Google Scholar 

  • KC Chou HB Shen (2006c) ArticleTitlePredicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers J Proteome Res 5 1888–1897 Occurrence Handle10.1021/pr060167c Occurrence Handle1:CAS:528:DC%2BD28XmvVeitr0%3D

    Article  CAS  Google Scholar 

  • P Du Y Li (2006) ArticleTitlePrediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence BMC Bioinformatics 7 518 Occurrence Handle17134515 Occurrence Handle10.1186/1471-2105-7-518 Occurrence Handle1:CAS:528:DC%2BD28XhtlWlsb7E

    Article  PubMed  CAS  Google Scholar 

  • QB Gao ZZ Wang C Yan YH Du (2005) ArticleTitlePrediction of protein subcellular location using a combined feature of sequence FEBS Lett 579 3444–3448 Occurrence Handle15949806 Occurrence Handle10.1016/j.febslet.2005.05.021 Occurrence Handle1:CAS:528:DC%2BD2MXlt1KjsL0%3D

    Article  PubMed  CAS  Google Scholar 

  • K Hofmann W Stoffel (1993) ArticleTitleA database of membrane spanning proteins segments Biol Chem 374 166

    Google Scholar 

  • W Kuhlbrandt D Wang (1994) ArticleTitleThree-dimensional structure of plant light-harvesting complex determined by electron crystallography Nature 350 130–134 Occurrence Handle10.1038/350130a0

    Article  Google Scholar 

  • Kuric L (2007) The digital language of amino acids. Amino Acids. doi: 10.1007/s00726-006-0476-x

  • J Kyte RF Doolittle (1982) ArticleTitleA simple method for displaying the hydroparthic character of a protein J Mol Biol 157 105–132 Occurrence Handle7108955 Occurrence Handle10.1016/0022-2836(82)90515-0 Occurrence Handle1:CAS:528:DyaL38Xks1yjtro%3D

    Article  PubMed  CAS  Google Scholar 

  • A Lempel J Ziv (1976) ArticleTitleOn the complexity of finite sequences IEEE Trans Inf Theory 22 75–81 Occurrence Handle10.1109/TIT.1976.1055501

    Article  Google Scholar 

  • H Liu M Wang KC Chou (2005) ArticleTitleLow-frequency Fourier spectrum for predicting membrane protein types Biochem Biophys Res Commun 336 737–739 Occurrence Handle16140260 Occurrence Handle10.1016/j.bbrc.2005.08.160 Occurrence Handle1:CAS:528:DC%2BD2MXhtVegtLfP

    Article  PubMed  CAS  Google Scholar 

  • O Martin AM Odlyzko S Wolfram (1984) ArticleTitleAlgebraic properties of cellular automata Commun Math Phys 93 219–258 Occurrence Handle10.1007/BF01223745

    Article  Google Scholar 

  • S Mondal R Bhavna BR Mohan S Ramakumar (2006) ArticleTitlePseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification J Theor Biol 243 252–260 Occurrence Handle16890961 Occurrence Handle10.1016/j.jtbi.2006.06.014 Occurrence Handle1:CAS:528:DC%2BD28XhtVygtbzM

    Article  PubMed  CAS  Google Scholar 

  • YX Pan ZZ Zhang ZM Guo L He (2003) ArticleTitleApplication of pseudo amino acid composition for predicting protein subcellular location: stochastic signal processing approach J Protein Chem 22 395–402 Occurrence Handle13678304 Occurrence Handle10.1023/A:1025350409648 Occurrence Handle1:CAS:528:DC%2BD3sXmsFejs7s%3D

    Article  PubMed  CAS  Google Scholar 

  • A Pautsch GE Schultz (1998) ArticleTitleStructure of the outer membrane protein A transmembrane domain Nat Struct Biol 5 1013–1017 Occurrence Handle9808047 Occurrence Handle10.1038/2983 Occurrence Handle1:CAS:528:DyaK1cXntlSksL0%3D

    Article  PubMed  CAS  Google Scholar 

  • B Rost P Fariselli R Casadio (1996) ArticleTitleTopology prediction for helical transmembrane proteins at 86% accuracy Protein Sci 5 1704–1718 Occurrence Handle8844859 Occurrence Handle1:CAS:528:DyaK28XkvVWgsrg%3D Occurrence Handle10.1002/pro.5560050824

    Article  PubMed  CAS  Google Scholar 

  • HB Shen KC Chou (2005a) ArticleTitlePredicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition Biochem Biophys Res Commun 337 752–756 Occurrence Handle1:CAS:528:DC%2BD2MXhtFCjs7%2FI

    CAS  Google Scholar 

  • HB Shen KC Chou (2005b) ArticleTitleUsing optimized evidence-theoretic K-nearest neighbor classifier and pseudo amino acid composition to predict membrane protein types Biochem Biophys Res Commun 334 288–292 Occurrence Handle10.1016/j.bbrc.2005.06.087 Occurrence Handle1:CAS:528:DC%2BD2MXmt1aqsLw%3D

    Article  CAS  Google Scholar 

  • HB Shen J Yang KC Chou (2006) ArticleTitleFuzzy KNN for predicting membrane protein types from pseudo amino acid composition J Theor Biol 240 9–13 Occurrence Handle16197963 Occurrence Handle10.1016/j.jtbi.2005.08.016 Occurrence Handle1:CAS:528:DC%2BD28Xjs1Knt70%3D

    Article  PubMed  CAS  Google Scholar 

  • HB Shen KC Chou (2006a) ArticleTitleEnsemble classifier for protein fold pattern recognition Bioinformatics 22 1717–1722 Occurrence Handle10.1093/bioinformatics/btl170 Occurrence Handle1:CAS:528:DC%2BD28Xotl2rsLY%3D

    Article  CAS  Google Scholar 

  • HB Shen KC Chou (2006b) ArticleTitleVirus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells Biopolymers 85 233–240 Occurrence Handle10.1002/bip.20640 Occurrence Handle1:CAS:528:DC%2BD2sXhvFWhs70%3D

    Article  CAS  Google Scholar 

  • HB Shen KC Chou (2007) ArticleTitleGpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins Protein Eng Des Sel 20 39–46 Occurrence Handle17244638 Occurrence Handle10.1093/protein/gzl053 Occurrence Handle1:CAS:528:DC%2BD2sXhvFWmtr8%3D

    Article  PubMed  CAS  Google Scholar 

  • JD Thompson DG Higgins TJ Gibson (1994) ArticleTitleCLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673–4680 Occurrence Handle7984417 Occurrence Handle10.1093/nar/22.22.4673 Occurrence Handle1:CAS:528:DyaK2MXitlSgu74%3D

    Article  PubMed  CAS  Google Scholar 

  • GE Tusnady I Simon (1998) ArticleTitlePrinciples governing amino acid composition of integral membrane proteins: application to topology prediction J Mol Biol 283 489–506 Occurrence Handle9769220 Occurrence Handle10.1006/jmbi.1998.2107 Occurrence Handle1:CAS:528:DyaK1cXntFWhtro%3D

    Article  PubMed  CAS  Google Scholar 

  • G von Heijine (1986) ArticleTitleThe distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology EMBO J 5 3021–3027

    Google Scholar 

  • von Neumann J (1966) Theory of self-reproducing automata. University of Illinois Press

  • M Wang J Yang GP Liu ZJ Xu KC Chou (2004) ArticleTitleWeighted-support vector machines for predicting membrane protein types based on pseudo amino acid composition Protein Eng Des Sel 17 509–516 Occurrence Handle15314209 Occurrence Handle10.1093/protein/gzh061 Occurrence Handle1:CAS:528:DC%2BD2cXos1GisLY%3D

    Article  PubMed  CAS  Google Scholar 

  • SQ Wang J Yang KC Chou (2006) ArticleTitleUsing stacked generalization to predict membrane protein types based on pseudo amino acid composition J Theor Biol 242 941–946 Occurrence Handle16806277 Occurrence Handle10.1016/j.jtbi.2006.05.006 Occurrence Handle1:CAS:528:DC%2BD28Xps1Oku70%3D

    Article  PubMed  CAS  Google Scholar 

  • Z Wen M Li Y Li Y Guo K Wang (2006) ArticleTitleDelaunay triangulation with partial least squares projection to latent structures: a model for G-protein coupled receptors classification and fast structure recognition Amino Acids 32 277–283 Occurrence Handle16729188 Occurrence Handle10.1007/s00726-006-0341-y Occurrence Handle1:CAS:528:DC%2BD2sXhtFyhtLY%3D

    Article  PubMed  CAS  Google Scholar 

  • S Wolfram (1984) ArticleTitleCellular automata as models of complexity Nature 311 419 Occurrence Handle10.1038/311419a0

    Article  Google Scholar 

  • S Wolfram (1986) ArticleTitleCellular automaton fluid: basic theory J Stat Phys 45 471 Occurrence Handle10.1007/BF01021083

    Article  Google Scholar 

  • X Xiao S Shao Y Ding Z Huang KC Chou (2005a) ArticleTitleUsing complexity measure factor to predict protein subcellular location Amino Acids 28 57–61 Occurrence Handle10.1007/s00726-004-0148-7 Occurrence Handle1:CAS:528:DC%2BD2MXhsVKqsro%3D

    Article  CAS  Google Scholar 

  • X Xiao S Shao Y Ding Z Huang KC Chou (2005b) ArticleTitleUsing cellular automata to generate image representation for biological sequences Amino Acids 28 29–35 Occurrence Handle10.1007/s00726-004-0154-9 Occurrence Handle1:CAS:528:DC%2BD2MXhsVKqs70%3D

    Article  CAS  Google Scholar 

  • X Xiao S Shao Y Ding Z Huang KC Chou (2006a) ArticleTitleUsing cellular automata images and pseudo amino acid composition to predict protein subcellular location Amino Acids 30 49–54 Occurrence Handle10.1007/s00726-005-0225-6 Occurrence Handle1:CAS:528:DC%2BD28XhsFCksrk%3D

    Article  CAS  Google Scholar 

  • X Xiao S Shao Z Huang KC Chou (2006b) ArticleTitleUsing pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor J Comput Chem 27 478–482 Occurrence Handle10.1002/jcc.20354 Occurrence Handle1:CAS:528:DC%2BD28XitFyqsr4%3D

    Article  CAS  Google Scholar 

  • SW Zhang Q Pan HC Zhang JY Shi (2006a) ArticleTitlePrediction protein homo-oligomer types by pseudo amino acid composition: approached with an improved feature extraction and naive Bayes feature fusion Amino Acids 30 461–468 Occurrence Handle10.1007/s00726-006-0263-8 Occurrence Handle1:CAS:528:DC%2BD28Xls1egsr0%3D

    Article  CAS  Google Scholar 

  • T Zhang Y Ding KC Chou (2006b) ArticleTitlePrediction of protein subcellular location using hydrophobic patterns of amino acid sequence Comput Biol Chem 30 367–371 Occurrence Handle10.1016/j.compbiolchem.2006.08.003 Occurrence Handle1:CAS:528:DC%2BD28XhtVSisrzN

    Article  CAS  Google Scholar 

  • Y Zheng S John (2004) ArticleTitleSVMtm: support vector machines to predict transmembrane segments J Comput Chem 25 632–636 Occurrence Handle10.1002/jcc.10411 Occurrence Handle1:CAS:528:DC%2BD2cXis1Kkt7c%3D

    Article  CAS  Google Scholar 

  • GP Zhou (1998) ArticleTitleAn intriguing controversy over protein structural class prediction J Protein Chem 17 729–738 Occurrence Handle9988519 Occurrence Handle10.1023/A:1020713915365 Occurrence Handle1:CAS:528:DyaK1MXnslaltw%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • GP Zhou N Assa-Munt (2001) ArticleTitleSome insights into protein structural class prediction Proteins Struct Funct Genet 44 57–59 Occurrence Handle11354006 Occurrence Handle10.1002/prot.1071 Occurrence Handle1:CAS:528:DC%2BD3MXktlSnsbk%3D

    Article  PubMed  CAS  Google Scholar 

  • GP Zhou K Doctor (2003) ArticleTitleSubcellular location prediction of apoptosis proteins Proteins Struct Funct Genet 50 44–48 Occurrence Handle12471598 Occurrence Handle10.1002/prot.10251 Occurrence Handle1:CAS:528:DC%2BD3sXlsVKmug%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • HY Zhou YQ Zhou (2003) ArticleTitlePredicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method Protein Sci 12 1547–1555 Occurrence Handle12824500 Occurrence Handle10.1110/ps.0305103 Occurrence Handle1:CAS:528:DC%2BD3sXltFeku7s%3D

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Chemistry, Sichuan University, Chengdu, Sichuan, China

    Y. Diao, D. Ma, Z. Wen, J. Yin, J. Xiang & M. Li

  2. State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China

    Y. Diao, Z. Wen & M. Li

Authors
  1. Y. Diao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Z. Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. Xiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. Li.

Additional information

Authors’ address: Menglong Li, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P.R. China

Rights and permissions

Reprints and permissions

About this article

Cite this article

Diao, Y., Ma, D., Wen, Z. et al. Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity. Amino Acids 34, 111–117 (2008). https://doi.org/10.1007/s00726-007-0550-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00726-007-0550-z

Search

Navigation