Skip to main content
SpringerLink
Log in

Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform

  • Published:
Amino Acids Aims and scope Submit manuscript

Summary.

As the potential drug targets, G-protein coupled receptors (GPCRs) and nuclear receptors (NRs) are the focuses in pharmaceutical research. It is of great practical significance to develop an automated and reliable method to facilitate the identification of novel receptors. In this study, a method of fast Fourier transform-based support vector machine was proposed to classify GPCRs and NRs from the hydrophobicity of proteins. The models for all the GPCR families and NR subfamilies were trained and validated using jackknife test and the results thus obtained are quite promising. Meanwhile, the performance of the method was evaluated on GPCR and NR independent datasets with good performance. The good results indicate the applicability of the method. Two web servers implementing the prediction are available at http://chem.scu.edu.cn/blast/Pred-GPCR and http://chem.scu.edu.cn/blast/Pred-NR.

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

  • SF Altschul W Gish W Miller (1990) ArticleTitleBasic local alignment search tool J Mol Biol 215 403–410 Occurrence Handle2231712 Occurrence Handle1:CAS:528:DyaK3MXitVGmsA%3D%3D Occurrence Handle10.1006/jmbi.1990.9999

    Article  PubMed  CAS  Google Scholar 

  • A Bateman L Coin R Durbin RD Finn V Hollich S Griffiths-Jones A Khanna M Marshall S Moxon ELL Sonnhammer DJ Studholme C Yeats SR Eddy (2004) ArticleTitleThe pfam protein families database Nucleic Acids Res 32 D138–D141 Occurrence Handle14681378 Occurrence Handle1:CAS:528:DC%2BD3sXhtVSru73I Occurrence Handle10.1093/nar/gkh121

    Article  PubMed  CAS  Google Scholar 

  • M Bhasin GPS Raghava (2004a) ArticleTitleGPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors Nucleic Acids Res 32 W383–W389 Occurrence Handle1:CAS:528:DC%2BD2cXlvFKnurw%3D Occurrence Handle10.1093/nar/gkh001

    Article  CAS  Google Scholar 

  • M Bhasin GPS Raghava (2004b) ArticleTitleClassification of nuclear receptors based on amino acid composition and dipeptide composition J Biol Chem 279 23262–23266 Occurrence Handle1:CAS:528:DC%2BD2cXkt1Gisbk%3D Occurrence Handle10.1074/jbc.M401932200

    Article  CAS  Google Scholar 

  • YD Cai GP Zhou KC Chou (2003) ArticleTitleSupport vector machines for predicting membrane protein types by using functional domain composition Biophys J 84 3257–3263 Occurrence Handle12719255 Occurrence Handle1:CAS:528:DC%2BD3sXjvFGju7o%3D Occurrence Handle10.1016/S0006-3495(03)70050-2

    Article  PubMed  CAS  Google Scholar 

  • YD Cai KC Chou (2005) ArticleTitleUsing functional domain composition to predict enzyme family classes J Proteome Res 4 109–111 Occurrence Handle15707365 Occurrence Handle1:CAS:528:DC%2BD2cXhtFWqsr%2FJ Occurrence Handle10.1021/pr049835p

    Article  PubMed  CAS  Google Scholar 

  • KC Chou (1988) ArticleTitleReview: Low-frequency collective motion in biomacromolecules and its biological functions Biophys Chem 30 3–48 Occurrence Handle3046672 Occurrence Handle1:CAS:528:DyaL1cXks1yru7k%3D Occurrence Handle10.1016/0301-4622(88)85002-6

    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 21 319–344 Occurrence Handle7567954 Occurrence Handle1:CAS:528:DyaK2MXls12rsb0%3D Occurrence Handle10.1002/prot.340210406

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  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 Handle1:CAS:528:DC%2BD38XovFKjurg%3D Occurrence Handle10.1074/jbc.M204161200

    Article  PubMed  CAS  Google Scholar 

  • KC Chou YD Cai (2004) ArticleTitlePredicting protein structural class by functional domain composition Biochem Biophys Res Commun 321 1007–1009 Occurrence Handle15358128 Occurrence Handle1:CAS:528:DC%2BD2cXmt1Ogtb0%3D Occurrence Handle10.1016/j.bbrc.2004.07.059

    Article  PubMed  CAS  Google Scholar 

  • KC Chou DW Elrod (2002) ArticleTitleBioinformatical analysis of G-protein-coupled receptors J Proteome Res 1 429–433 Occurrence Handle12645914 Occurrence Handle1:CAS:528:DC%2BD38XkvVygu7k%3D Occurrence Handle10.1021/pr025527k

    Article  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 Handle1:CAS:528:DyaK2MXosFentb8%3D

    PubMed  CAS  Google Scholar 

  • I Cosic (1994) ArticleTitleMacromolecular bioactivity: is it resonant interaction between macromolecules? – Theory and applications IEEE Trans Biomed Eng 41 1101–1114 Occurrence Handle7851912 Occurrence Handle1:STN:280:DyaK2M7lsVymtg%3D%3D Occurrence Handle10.1109/10.335859

    Article  PubMed  CAS  Google Scholar 

  • DW Elrod KC Chou (2002) ArticleTitleA study on the correlation of G-protein coupled receptor types with amino acid composition Protein Eng 15 713–715 Occurrence Handle12456868 Occurrence Handle1:CAS:528:DC%2BD38XptlOhtLg%3D Occurrence Handle10.1093/protein/15.9.713

    Article  PubMed  CAS  Google Scholar 

  • J Fauchére V Pliška (1983) ArticleTitleHydrophobic parameters Φ of amino-acid side chains from the partitioning of n-acetyl-amino-acid amides Eur J Med Chem Chim Ther 18 369–375

    Google Scholar 

  • Y Gao SH Shao X Xiao YS Ding YS Huang ZD Huang KC Chou (2005) ArticleTitleUsing pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter Amino Acids 28 373–376 Occurrence Handle15889221 Occurrence Handle1:CAS:528:DC%2BD2MXlt1Kmurw%3D Occurrence Handle10.1007/s00726-005-0206-9

    Article  PubMed  CAS  Google Scholar 

  • R Grantham (1974) ArticleTitleAmino acid difference formular to help explain protein evolution Science 185 862–864 Occurrence Handle4843792 Occurrence Handle1:CAS:528:DyaE2cXlsVOiuro%3D

    PubMed  CAS  Google Scholar 

  • H Gronemeyer V Laudet (1995) ArticleTitleTranscription factors 3: nuclear receptors Protein Profile 2 1173–1308 Occurrence Handle8681033 Occurrence Handle1:CAS:528:DyaK28XitVOqu74%3D

    PubMed  CAS  Google Scholar 

  • T Gudermann B Nürnberg G Schultz (1995) ArticleTitleReceptors and G proteins as primary components of transmembrane signal transduction. Part 1. G-protein-coupled receptors: Structure and function J Mol Med 73 51–63 Occurrence Handle7627630 Occurrence Handle1:CAS:528:DyaK2MXksF2gtrk%3D Occurrence Handle10.1007/BF00270578

    Article  PubMed  CAS  Google Scholar 

  • YZ Guo ML Li KL Wang ZN Wen ML Lu LX Liu L Jiang (2005) ArticleTitleFast Fourier transform-based support vector machine for prediction of G-protein coupled receptor subfamilies Acta Biochim Biophys Sin 37 759–766 Occurrence Handle16270155 Occurrence Handle1:CAS:528:DC%2BD2MXhtlWnsbbL Occurrence Handle10.1111/j.1745-7270.2005.00110.x

    Article  PubMed  CAS  Google Scholar 

  • T Hiramoto W Nemoto T Kikuchi N Fujita (2002) ArticleTitleConstruction of hypothetical three-dimensional structure of P2Y1 receptor based on Fourier transform analysis J Protein Chem 21 537–545 Occurrence Handle12638656 Occurrence Handle1:CAS:528:DC%2BD3sXhtVGmu7s%3D Occurrence Handle10.1023/A:1022429722651

    Article  PubMed  CAS  Google Scholar 

  • F Horn E Bettler L Oliveira F Campagne FE Cohen G Vriend (2003) ArticleTitleGPCRDB information system for G protein coupled receptors Nucleic Acids Res 31 294–297 Occurrence Handle12520006 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSmsLs%3D Occurrence Handle10.1093/nar/gkg103

    Article  PubMed  CAS  Google Scholar 

  • F Horn G Vriend FE Cohen (2001) ArticleTitleCollecting and harvesting biological data: the GPCRDB and NucleaRDB information systems Nucleic Acids Res 29 346–349 Occurrence Handle11125133 Occurrence Handle1:CAS:528:DC%2BD3MXjtlWlsLY%3D Occurrence Handle10.1093/nar/29.1.346

    Article  PubMed  CAS  Google Scholar 

  • SJ Hua ZR Sun (2001) ArticleTitleSupport vector machine approach for protein subcellular localization prediction Bioinformatics 17 721–728 Occurrence Handle11524373 Occurrence Handle1:CAS:528:DC%2BD3MXntFKjsb0%3D Occurrence Handle10.1093/bioinformatics/17.8.721

    Article  PubMed  CAS  Google Scholar 

  • Y Huang J Cai L Ji YD Li (2004) ArticleTitleClassifying G-protein coupled receptors with bagging classification tree Comput Biol Chem 28 39–49 Occurrence Handle1:CAS:528:DC%2BD2cXhtVejtLzN Occurrence Handle10.1016/j.compbiolchem.2004.08.001

    Article  CAS  Google Scholar 

  • R Karchin K Karplus D Haussler (2002) ArticleTitleClassifying G-protein coupled receptors with support vector machines Bioinformatics 18 147–159 Occurrence Handle11836223 Occurrence Handle1:CAS:528:DC%2BD38Xhs1elu7w%3D Occurrence Handle10.1093/bioinformatics/18.1.147

    Article  PubMed  CAS  Google Scholar 

  • K Katoh K Misawa K Kuma T Miyata (2002) ArticleTitleMAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res 30 3059–3066 Occurrence Handle12136088 Occurrence Handle1:CAS:528:DC%2BD38XlslOqu7s%3D Occurrence Handle10.1093/nar/gkf436

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • H Liu J Yang JG Ling KC Chou (2005b) ArticleTitlePrediction of protein signal sequences and their cleavage sites by statistical rulers Biochem Biophys Res Commun 338 1005–1011 Occurrence Handle1:CAS:528:DC%2BD2MXht1Wjur3F Occurrence Handle10.1016/j.bbrc.2005.10.046

    Article  CAS  Google Scholar 

  • AJ Mandell KA Selz MF Shlesinger (1997) ArticleTitleWavelet transformation of protein hydrophobicity sequences suggests their memberships in structural families Physica (A) 244 254–262 Occurrence Handle1:CAS:528:DyaK2sXmtFKktb0%3D

    CAS  Google Scholar 

  • DJ Mangelsdorf C Thummel M Beato P Herrlich G Schütz K Umesono B Blumberg P Kastner M Mark P Chambon RM Evans (1995) ArticleTitleThe nuclear receptor superfamilily: the second decade Cell 83 835–839 Occurrence Handle8521507 Occurrence Handle1:CAS:528:DyaK2MXhtVSnu7nJ Occurrence Handle10.1016/0092-8674(95)90199-X

    Article  PubMed  CAS  Google Scholar 

  • BW Matthews (1975) ArticleTitleComparison of predicted and observed secondary structure of T4 phage lysozyme Biochim Biophys Acta 405 442–451 Occurrence Handle1180967 Occurrence Handle1:CAS:528:DyaE2MXlslCksbk%3D

    PubMed  CAS  Google Scholar 

  • M Novic J Zupan (1995) ArticleTitleInvestigation of infrared spectra-structure correlation using kohonen and counterpropagation neural network J Chem Inf Comput Sci 35 454–466 Occurrence Handle1:CAS:528:DyaK2MXls1yksL4%3D Occurrence Handle10.1021/ci00025a013

    Article  CAS  Google Scholar 

  • K Palczewski T Kumasaka T Hori CA Behnke H Motoshima BA Fox I Le Trong DC Teller T Okada RE Stenkamp M Yamamoto M Miyano (2000) ArticleTitleCrystal structure of rhodopsin: a G-protein coupled receptor Science 289 739–745 Occurrence Handle10926528 Occurrence Handle1:CAS:528:DC%2BD3cXlslOqs78%3D Occurrence Handle10.1126/science.289.5480.739

    Article  PubMed  CAS  Google Scholar 

  • PK Papasaikas PG Bagos ZI Litou VJ Promponas SJ Hamodrakas (2004) ArticleTitlePRED-GPCR: GPCR recognition and family classification server Nucleic Acids Res 32 W380–W382 Occurrence Handle15215415 Occurrence Handle1:CAS:528:DC%2BD2cXlvFKnur8%3D Occurrence Handle10.1093/nar/gkh180

    Article  PubMed  CAS  Google Scholar 

  • WR Pearson DJ Lipman (1988) ArticleTitleImproved tool for biological sequence comparison Proc Natl Acad Sci USA 85 2444–2448 Occurrence Handle3162770 Occurrence Handle1:CAS:528:DyaL1cXktFyit78%3D Occurrence Handle10.1073/pnas.85.8.2444

    Article  PubMed  CAS  Google Scholar 

  • B Qian OS Soyer RR Neubig RA Goldstein (2003) ArticleTitleDepicting a protein’s two faces: GPCR classification by phylogenetic tree-based HMMs FEBS Lett 554 95–99 Occurrence Handle14596921 Occurrence Handle1:CAS:528:DC%2BD3sXosVymu7k%3D Occurrence Handle10.1016/S0014-5793(03)01112-8

    Article  PubMed  CAS  Google Scholar 

  • M Robinson-Rechavi V Laude (2003) ArticleTitleBioinformatics of nuclear receptors Methods Enzymol 364 95–118 Occurrence Handle14631841 Occurrence Handle1:CAS:528:DC%2BD2cXos1yjsg%3D%3D

    PubMed  CAS  Google Scholar 

  • HB Shen KC Chou (2005a) 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 Handle1:CAS:528:DC%2BD2MXmt1aqsLw%3D Occurrence Handle10.1016/j.bbrc.2005.06.087

    Article  CAS  Google Scholar 

  • HB Shen KC Chou (2005b) 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 Occurrence Handle10.1016/j.bbrc.2005.09.117

    Article  CAS  Google Scholar 

  • AJ Shepherd D Gorse JM Thornton (2003) ArticleTitleA novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks Proteins 50 290–302 Occurrence Handle12486723 Occurrence Handle1:CAS:528:DC%2BD3sXjslaksA%3D%3D Occurrence Handle10.1002/prot.10290

    Article  PubMed  CAS  Google Scholar 

  • CH Trad Q Fang I Cosic (2002) ArticleTitleProtein sequence comparison based on the wavelet transform approach Protein Eng 15 193–203 Occurrence Handle11932490 Occurrence Handle10.1093/protein/15.3.193

    Article  PubMed  Google Scholar 

  • 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 Handle1:CAS:528:DC%2BD2cXos1GisLY%3D Occurrence Handle10.1093/protein/gzh061

    Article  PubMed  CAS  Google Scholar 

  • X Xiao SH Shao YS Ding ZD Huang KC Chou (2006) ArticleTitleUsing cellular automata images and pseudo amino acid composition to predict protein sub-cellular location Amino Acids 30 49–54 Occurrence Handle16044193 Occurrence Handle1:CAS:528:DC%2BD28XhsFCksrk%3D Occurrence Handle10.1007/s00726-005-0225-6

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

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

    Y.-Z. Guo, M. Li, M. Lu, Z. Wen, K. Wang, G. Li & J. Wu

  2. State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China

    Y.-Z. Guo, M. Li & Z. Wen

Authors
  1. Y.-Z. Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Z. Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. K. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. G. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. J. Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Guo, YZ., Li, M., Lu, M. et al. Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform. Amino Acids 30, 397–402 (2006). https://doi.org/10.1007/s00726-006-0332-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00726-006-0332-z

Search

Navigation