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Volumn 33, Issue 8, 2015, Pages 1731-1742

IUbiq-Lys: Prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model

Author keywords

Chou's PseAAC; gray system model; SVM; ubiquitination; web server, iUbiq Lys

Indexed keywords

LYSINE; PROTEIN;

EID: 84930570742     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2014.968875     Document Type: Article
Times cited : (167)

References (96)
  • 2
    • 0038705861 scopus 로고    scopus 로고
    • Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition
    • Cai, Y. D. (2003). Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition. Biochemical and Biophysical Research Communications, 305, 407-411.
    • (2003) Biochemical and Biophysical Research Communications , vol.305 , pp. 407-411
    • Cai, Y.D.1
  • 3
    • 84862641013 scopus 로고    scopus 로고
    • Prediction of lysine ubiquitination with mRMR feature selection and analysis
    • Cai, Y., Huang, T., Hu, L., Shi, X., Xie, L., & Li, Y. (2012). Prediction of lysine ubiquitination with mRMR feature selection and analysis. Amino Acids, 42, 1387-1395.
    • (2012) Amino Acids , vol.42 , pp. 1387-1395
    • Cai, Y.1    Huang, T.2    Hu, L.3    Shi, X.4    Xie, L.5    Li, Y.6
  • 4
    • 0038636605 scopus 로고    scopus 로고
    • Support vector machines for predicting membrane protein types by using functional domain composition
    • Cai, Y. D., Zhou, G. P., & Chou, K. C. (2003). Support vector machines for predicting membrane protein types by using functional domain composition. Biophysical Journal, 84, 3257-3263.
    • (2003) Biophysical Journal , vol.84 , pp. 3257-3263
    • Cai, Y.D.1    Zhou, G.P.2    Chou, K.C.3
  • 5
    • 84875576158 scopus 로고    scopus 로고
    • Propy: A tool to generate various modes of Chou's PseAAC
    • Cao, D. S., Xu, Q. S., & Liang, Y. Z. (2013). Propy: A tool to generate various modes of Chou's PseAAC. Bioinformatics, 29, 960-962.
    • (2013) Bioinformatics , vol.29 , pp. 960-962
    • Cao, D.S.1    Xu, Q.S.2    Liang, Y.Z.3
  • 7
    • 79960909253 scopus 로고    scopus 로고
    • Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs
    • Chen, Z., Chen, Y. Z., Wang, X. F., Wang, C., Yan, R. X., & Zhang, Z. (2011). Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs. PLoS ONE, 6, e22930.
    • (2011) PLoS ONE , vol.6 , pp. e22930
    • Chen, Z.1    Chen, Y.Z.2    Wang, X.F.3    Wang, C.4    Yan, R.X.5    Zhang, Z.6
  • 8
    • 84921500317 scopus 로고    scopus 로고
    • ITIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition
    • Chen, W., Feng, P. M., & Deng, E. Z. (2014). iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition. Analytical Biochemistry, 462, 76-83.
    • (2014) Analytical Biochemistry , vol.462 , pp. 76-83
    • Chen, W.1    Feng, P.M.2    Deng, E.Z.3
  • 9
    • 84876053736 scopus 로고    scopus 로고
    • IRSpot-PseDNC: Identify recombination spots with pseudo dinucleotide composition
    • Chen, W., Feng, P. M., & Lin, H. (2013). iRSpot-PseDNC: Identify recombination spots with pseudo dinucleotide composition. Nucleic Acids Research, 41, e68.
    • (2013) Nucleic Acids Research , vol.41 , pp. e68
    • Chen, W.1    Feng, P.M.2    Lin, H.3
  • 10
    • 84900463301 scopus 로고    scopus 로고
    • PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition
    • Chen, W., Lei, T. Y., Jin, D. C., & Lin, H. (2014). PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition. Analytical Biochemistry, 456, 53-60.
    • (2014) Analytical Biochemistry , vol.456 , pp. 53-60
    • Chen, W.1    Lei, T.Y.2    Jin, D.C.3    Lin, H.4
  • 11
    • 84870215870 scopus 로고    scopus 로고
    • Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's pseudo amino acid composition
    • Chen, Y. K., & Li, K. B. (2013). Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's pseudo amino acid composition. Journal of Theoretical Biology, 318, 1-12.
    • (2013) Journal of Theoretical Biology , vol.318 , pp. 1-12
    • Chen, Y.K.1    Li, K.B.2
  • 12
    • 84868128310 scopus 로고    scopus 로고
    • INuc-PhysChem: A sequence-based predictor for identifying nucleosomes via physicochemical properties
    • Chen, W., Lin, H., Feng, P. M., & Ding, C. (2012). iNuc-PhysChem: A sequence-based predictor for identifying nucleosomes via physicochemical properties. PLoS ONE, 7, e47843.
    • (2012) PLoS ONE , vol.7 , pp. e47843
    • Chen, W.1    Lin, H.2    Feng, P.M.3    Ding, C.4
  • 13
    • 0027219970 scopus 로고
    • A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins
    • Chou, K. C. (1993). A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. Journal of Biological Chemistry, 268, 16938-16948.
    • (1993) Journal of Biological Chemistry , vol.268 , pp. 16938-16948
    • Chou, K.C.1
  • 14
    • 0028904113 scopus 로고
    • The convergence-divergence duality in lectin domains of selectin family and its implications
    • Chou, K. C. (1995a). The convergence-divergence duality in lectin domains of selectin family and its implications. FEBS Letters, 363, 123-126.
    • (1995) FEBS Letters , vol.363 , pp. 123-126
    • Chou, K.C.1
  • 15
    • 0029076524 scopus 로고
    • A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase
    • Chou, K. C. (1995b). A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase. Protein Science, 4, 1365-1383.
    • (1995) Protein Science , vol.4 , pp. 1365-1383
    • Chou, K.C.1
  • 16
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein cellular attributes using pseudo amino acid composition
    • Chou, K. C. (2001a). Prediction of protein cellular attributes using pseudo amino acid composition. PROTEINS: Structure, Function, and Genetics, 43, 246-255.
    • (2001) PROTEINS: Structure, Function, and Genetics , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 17
    • 0035030201 scopus 로고    scopus 로고
    • Using subsite coupling to predict signal peptides
    • Chou, K. C. (2001b). Using subsite coupling to predict signal peptides. Protein Engineering Design and Selection, 14, 75-79.
    • (2001) Protein Engineering Design and Selection , vol.14 , pp. 75-79
    • Chou, K.C.1
  • 18
    • 3242792729 scopus 로고    scopus 로고
    • Structural bioinformatics and its impact to biomedical science
    • Chou, K. C. (2004). Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry, 11, 2105-2134.
    • (2004) Current Medicinal Chemistry , vol.11 , pp. 2105-2134
    • Chou, K.C.1
  • 19
    • 12744279642 scopus 로고    scopus 로고
    • Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    • Chou, K. C. (2005). Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics, 21, 10-19.
    • (2005) Bioinformatics , vol.21 , pp. 10-19
    • Chou, K.C.1
  • 20
    • 79951518208 scopus 로고    scopus 로고
    • Some remarks on protein attribute prediction and pseudo amino acid composition
    • Chou, K. C. (2011). Some remarks on protein attribute prediction and pseudo amino acid composition. Journal of Theoretical Biology, 273, 236-247.
    • (2011) Journal of Theoretical Biology , vol.273 , pp. 236-247
    • Chou, K.C.1
  • 21
    • 84877758233 scopus 로고    scopus 로고
    • Some remarks on predicting multi-label attributes in molecular biosystems
    • Chou, K. C. (2013). Some remarks on predicting multi-label attributes in molecular biosystems. Molecular BioSystems, 9, 1092-1100.
    • (2013) Molecular BioSystems , vol.9 , pp. 1092-1100
    • Chou, K.C.1
  • 22
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • Chou, K. C., & Shen, H. B. (2007). Recent progress in protein subcellular location prediction. Analytical Biochemistry, 370, 1-16.
    • (2007) Analytical Biochemistry , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 24
    • 0001829246 scopus 로고
    • Introduction to grey system theory
    • Deng, J. L. (1989). Introduction to grey system theory. The Journal of Grey System, 1, 1-24.
    • (1989) The Journal of Grey System , vol.1 , pp. 1-24
    • Deng, J.L.1
  • 25
    • 84903592187 scopus 로고    scopus 로고
    • ICTX-Type: A sequence-based predictor for identifying the types of conotoxins in targeting ion channels
    • Ding, H., Deng, E. Z., Yuan, L. F., Liu, L., & Lin, H. (2014). iCTX-Type: A sequence-based predictor for identifying the types of conotoxins in targeting ion channels. BioMed Research International 2014, 286419.
    • (2014) BioMed Research International , vol.2014 , pp. 286419
    • Ding, H.1    Deng, E.Z.2    Yuan, L.F.3    Liu, L.4    Lin, H.5
  • 26
    • 84895429516 scopus 로고    scopus 로고
    • PseAAC-general: Fast building various modes of general form of Chou's pseudo-amino acid composition for large-scale protein datasets
    • Du, P., Gu, S., & Jiao, Y. (2014). PseAAC-general: Fast building various modes of general form of Chou's pseudo-amino acid composition for large-scale protein datasets. International Journal of Molecular Sciences, 15, 3495-3506.
    • (2014) International Journal of Molecular Sciences , vol.15 , pp. 3495-3506
    • Du, P.1    Gu, S.2    Jiao, Y.3
  • 27
    • 84859932176 scopus 로고    scopus 로고
    • PseAAC-builder: A cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions
    • Du, P., Wang, X., Xu, C., & Gao, Y. (2012). PseAAC-builder: A cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. Analytical Biochemistry, 425, 117-119.
    • (2012) Analytical Biochemistry , vol.425 , pp. 117-119
    • Du, P.1    Wang, X.2    Xu, C.3    Gao, Y.4
  • 28
    • 33646568767 scopus 로고    scopus 로고
    • Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction
    • Du, Q. S., Jiang, Z. Q., He, W. Z., & Li, D. P. (2006). Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction. Journal of Biomolecular Structure and Dynamics, 23, 635-640.
    • (2006) Journal of Biomolecular Structure and Dynamics , vol.23 , pp. 635-640
    • Du, Q.S.1    Jiang, Z.Q.2    He, W.Z.3    Li, D.P.4
  • 29
    • 77649337793 scopus 로고    scopus 로고
    • Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses
    • Esmaeili, M., Mohabatkar, H., & Mohsenzadeh, S. (2010). Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses. Journal of Theoretical Biology, 263, 203-209.
    • (2010) Journal of Theoretical Biology , vol.263 , pp. 203-209
    • Esmaeili, M.1    Mohabatkar, H.2    Mohsenzadeh, S.3
  • 30
    • 84896470341 scopus 로고    scopus 로고
    • INR-Drug: Predicting the interaction of drugs with nuclear receptors in cellular networking
    • Fan, Y. N., Xiao, X., & Min, J. L. (2014). iNR-Drug: Predicting the interaction of drugs with nuclear receptors in cellular networking. International Journal of Molecular Sciences, 15, 4915-4937.
    • (2014) International Journal of Molecular Sciences , vol.15 , pp. 4915-4937
    • Fan, Y.N.1    Xiao, X.2    Min, J.L.3
  • 32
    • 84885640993 scopus 로고    scopus 로고
    • IHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
    • Feng, P. M., Chen, W., & Lin, H. (2013). iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition. Analytical Biochemistry, 442, 118-125.
    • (2013) Analytical Biochemistry , vol.442 , pp. 118-125
    • Feng, P.M.1    Chen, W.2    Lin, H.3
  • 33
    • 84896693437 scopus 로고    scopus 로고
    • A short survey on genetic sequences, Chou's pseudo amino acid composition and its combination with fuzzy set theory
    • Retrieved from
    • Georgiou, D. N., Karakasidis, T. E., & Megaritis, A. C. (2013). A short survey on genetic sequences, Chou's pseudo amino acid composition and its combination with fuzzy set theory. The Open Bioinformatics Journal, 7, 41-48. Retrieved from http://www.benthamscience.com/open/tobioij/articles/V007/SI0025TOBIOIJ/41TOBIOIJ.pdf
    • (2013) The Open Bioinformatics Journal , vol.7 , pp. 41-48
    • Georgiou, D.N.1    Karakasidis, T.E.2    Megaritis, A.C.3
  • 34
    • 84896463976 scopus 로고    scopus 로고
    • INuc-PseKNC: A sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
    • Guo, S. H., Deng, E. Z., Xu, L. Q., Ding, H., & Lin, H. (2014). iNuc-PseKNC: A sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Bioinformatics, 30, 1522-1529.
    • (2014) Bioinformatics , vol.30 , pp. 1522-1529
    • Guo, S.H.1    Deng, E.Z.2    Xu, L.Q.3    Ding, H.4    Lin, H.5
  • 35
    • 27144529182 scopus 로고    scopus 로고
    • Ubiquitylation and cell signaling
    • Haglund, K., & Dikic, I. (2005). Ubiquitylation and cell signaling. The EMBO Journal, 24, 3353-3359.
    • (2005) The EMBO Journal , vol.24 , pp. 3353-3359
    • Haglund, K.1    Dikic, I.2
  • 36
    • 84886433492 scopus 로고    scopus 로고
    • Predicting anticancer peptides with Chou's pseudo amino acid composition and investigating their mutagenicity via Ames test
    • Hajisharifi, Z., Piryaiee, M., Mohammad Beigi, M., Behbahani, M., & Mohabatkar, H. (2014). Predicting anticancer peptides with Chou's pseudo amino acid composition and investigating their mutagenicity via Ames test. Journal of Theoretical Biology, 341, 34-40.
    • (2014) Journal of Theoretical Biology , vol.341 , pp. 34-40
    • Hajisharifi, Z.1    Piryaiee, M.2    Mohammad Beigi, M.3    Behbahani, M.4    Mohabatkar, H.5
  • 37
    • 84890876239 scopus 로고    scopus 로고
    • A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC
    • Han, G. S., Yu, Z. G., & Anh, V. (2014). A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC. Journal of Theoretical Biology, 344, 31-39.
    • (2014) Journal of Theoretical Biology , vol.344 , pp. 31-39
    • Han, G.S.1    Yu, Z.G.2    Anh, V.3
  • 38
    • 84858833657 scopus 로고    scopus 로고
    • Discriminating outer membrane proteins with fuzzy K-nearest neighbor algorithms based on the general form of Chou's PseAAC
    • Hayat, M., & Khan, A. (2012). Discriminating outer membrane proteins with fuzzy K-nearest neighbor algorithms based on the general form of Chou's PseAAC. Protein and Peptide Letters, 19, 411-421.
    • (2012) Protein and Peptide Letters , vol.19 , pp. 411-421
    • Hayat, M.1    Khan, A.2
  • 39
  • 40
    • 34248379575 scopus 로고    scopus 로고
    • Ubiquitin and ubiquitin-like proteins in protein regulation
    • Herrmann, J., Lerman, L. O., & Lerman, A. (2007). Ubiquitin and ubiquitin-like proteins in protein regulation. Circulation Research, 100, 1276-1291.
    • (2007) Circulation Research , vol.100 , pp. 1276-1291
    • Herrmann, J.1    Lerman, L.O.2    Lerman, A.3
  • 43
    • 0141442586 scopus 로고    scopus 로고
    • Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins
    • Hicke, L., & Dunn, R. (2003). Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. Annual Review of Cell and Developmental Biology, 19, 141-172.
    • (2003) Annual Review of Cell and Developmental Biology , vol.19 , pp. 141-172
    • Hicke, L.1    Dunn, R.2
  • 44
    • 33748991453 scopus 로고    scopus 로고
    • Ubiquitin and ubiquitin-like proteins in cancer pathogenesis
    • Hoeller, D., Hecker, C. M., & Dikic, I. (2006). Ubiquitin and ubiquitin-like proteins in cancer pathogenesis. Nature Reviews Cancer, 6, 776-788.
    • (2006) Nature Reviews Cancer , vol.6 , pp. 776-788
    • Hoeller, D.1    Hecker, C.M.2    Dikic, I.3
  • 45
    • 84876592631 scopus 로고    scopus 로고
    • Signal propagation in protein interaction network during colorectal cancer progression
    • Jiang, Y., Huang, T., Chen, L., & Gao, Y. F. (2013). Signal propagation in protein interaction network during colorectal cancer progression. BioMed Research International 2013, 287019.
    • (2013) BioMed Research International 2013 , pp. 287019
    • Jiang, Y.1    Huang, T.2    Chen, L.3    Gao, Y.F.4
  • 47
    • 78650673337 scopus 로고    scopus 로고
    • Prediction of apoptosis protein locations with genetic algorithms and support vector machines through a new mode of pseudo amino acid composition
    • Kandaswamy, K. K., Pugalenthi, G., Moller, S., Hartmann, E., Kalies, K. U., Suganthan, P. N., & Martinetz, T. (2010). Prediction of apoptosis protein locations with genetic algorithms and support vector machines through a new mode of pseudo amino acid composition. Protein and Peptide Letters, 17, 1473-1479.
    • (2010) Protein and Peptide Letters , vol.17 , pp. 1473-1479
    • Kandaswamy, K.K.1    Pugalenthi, G.2    Moller, S.3    Hartmann, E.4    Kalies, K.U.5    Suganthan, P.N.6    Martinetz, T.7
  • 48
    • 84876370111 scopus 로고    scopus 로고
    • Predicting antibacterial peptides by the concept of Chou's pseudo-amino acid composition and machine learning methods
    • Khosravian, M., Faramarzi, F. K., Beigi, M. M., Behbahani, M., & Mohabatkar, H. (2013). Predicting antibacterial peptides by the concept of Chou's pseudo-amino acid composition and machine learning methods. Protein and Peptide Letters, 20, 180-186.
    • (2013) Protein and Peptide Letters , vol.20 , pp. 180-186
    • Khosravian, M.1    Faramarzi, F.K.2    Beigi, M.M.3    Behbahani, M.4    Mohabatkar, H.5
  • 49
    • 84890593591 scopus 로고    scopus 로고
    • Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition
    • Kong, L., Zhang, L., & Lv, J. (2014). Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition. Journal of Theoretical Biology, 344, 12-18.
    • (2014) Journal of Theoretical Biology , vol.344 , pp. 12-18
    • Kong, L.1    Zhang, L.2    Lv, J.3
  • 51
    • 80052855771 scopus 로고    scopus 로고
    • IDNA-Prot: Identification of DNA binding proteins using random forest with grey model
    • Lin, W. Z., Fang, J. A., & Xiao, X. (2011). iDNA-Prot: Identification of DNA binding proteins using random forest with grey model. PLoS ONE, 6, e24756.
    • (2011) PLoS ONE , vol.6 , pp. e24756
    • Lin, W.Z.1    Fang, J.A.2    Xiao, X.3
  • 52
    • 84874928986 scopus 로고    scopus 로고
    • ILoc-Animal: A multi-label learning classifier for predicting subcellular localization of animal proteins
    • Lin, W. Z., Fang, J. A., & Xiao, X. (2013). iLoc-Animal: A multi-label learning classifier for predicting subcellular localization of animal proteins. Molecular BioSystems, 9, 634-644.
    • (2013) Molecular BioSystems , vol.9 , pp. 634-644
    • Lin, W.Z.1    Fang, J.A.2    Xiao, X.3
  • 53
    • 84892972298 scopus 로고    scopus 로고
    • Protein remote homology detection by combining Chou's pseudo amino acid composition and profile-based protein representation
    • Liu, B., Wang, X., Zou, Q., Dong, Q., & Chen, Q. (2013). Protein remote homology detection by combining Chou's pseudo amino acid composition and profile-based protein representation. Molecular Informatics, 32, 775-782.
    • (2013) Molecular Informatics , vol.32 , pp. 775-782
    • Liu, B.1    Wang, X.2    Zou, Q.3    Dong, Q.4    Chen, Q.5
  • 54
    • 84906975785 scopus 로고    scopus 로고
    • IDNA-Prot|dis: Identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition
    • Liu, B., Xu, J., Lan, X., Xu, R., & Zhou, J. (2014). iDNA-Prot|dis: Identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition. PLoS ONE, 9, e106691.
    • (2014) PLoS ONE , vol.9 , pp. e106691
    • Liu, B.1    Xu, J.2    Lan, X.3    Xu, R.4    Zhou, J.5
  • 55
    • 84892954329 scopus 로고    scopus 로고
    • Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection
    • Liu, B., Zhang, D., Xu, R., Xu, J., Wang, X., & Chen, Q. (2014). Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. Bioinformatics, 30, 472-479.
    • (2014) Bioinformatics , vol.30 , pp. 472-479
    • Liu, B.1    Zhang, D.2    Xu, R.3    Xu, J.4    Wang, X.5    Chen, Q.6
  • 56
    • 84863695726 scopus 로고    scopus 로고
    • Predicting plant protein subcellular multi-localization by Chou's PseAAC formulation based multi-label homolog knowledge transfer learning
    • Mei, S. (2012a). Predicting plant protein subcellular multi-localization by Chou's PseAAC formulation based multi-label homolog knowledge transfer learning. Journal of Theoretical Biology, 310, 80-87.
    • (2012) Journal of Theoretical Biology , vol.310 , pp. 80-87
    • Mei, S.1
  • 57
    • 80155143429 scopus 로고    scopus 로고
    • Multi-kernel transfer learning based on Chou's PseAAC formulation for protein submitochondria localization
    • Mei, S. (2012b). Multi-kernel transfer learning based on Chou's PseAAC formulation for protein submitochondria localization. Journal of Theoretical Biology, 293, 121-130.
    • (2012) Journal of Theoretical Biology , vol.293 , pp. 121-130
    • Mei, S.1
  • 58
    • 77958497871 scopus 로고    scopus 로고
    • Prediction of cyclin proteins using Chou's pseudo amino acid composition
    • Mohabatkar, H. (2010). Prediction of cyclin proteins using Chou's pseudo amino acid composition. Protein and Peptide Letters, 17, 1207-1214.
    • (2010) Protein and Peptide Letters , vol.17 , pp. 1207-1214
    • Mohabatkar, H.1
  • 59
    • 84873572573 scopus 로고    scopus 로고
    • Prediction of allergenic proteins by means of the concept of Chou's pseudo amino acid composition and a machine learning approach
    • Mohabatkar, H., Beigi, M. M., Abdolahi, K., & Mohsenzadeh, S. (2013). Prediction of allergenic proteins by means of the concept of Chou's pseudo amino acid composition and a machine learning approach. Medicinal Chemistry, 9, 133-137.
    • (2013) Medicinal Chemistry , vol.9 , pp. 133-137
    • Mohabatkar, H.1    Beigi, M.M.2    Abdolahi, K.3    Mohsenzadeh, S.4
  • 60
    • 79955564229 scopus 로고    scopus 로고
    • Prediction of GABA(A) receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine
    • Mohabatkar, H., Mohammad Beigi, M., & Esmaeili, A. (2011). Prediction of GABA(A) receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine. Journal of Theoretical Biology, 281, 18-23.
    • (2011) Journal of Theoretical Biology , vol.281 , pp. 18-23
    • Mohabatkar, H.1    Mohammad Beigi, M.2    Esmaeili, A.3
  • 61
    • 84855690179 scopus 로고    scopus 로고
    • Prediction of metalloproteinase family based on the concept of Chou's pseudo amino acid composition using a machine learning approach
    • Mohammad Beigi, M., Behjati, M., & Mohabatkar, H. (2011). Prediction of metalloproteinase family based on the concept of Chou's pseudo amino acid composition using a machine learning approach. Journal of Structural and Functional Genomics, 12, 191-197.
    • (2011) Journal of Structural and Functional Genomics , vol.12 , pp. 191-197
    • Mohammad Beigi, M.1    Behjati, M.2    Mohabatkar, H.3
  • 62
    • 43149097851 scopus 로고    scopus 로고
    • Genetic programming for creating Chou's pseudo amino acid based features for submitochondria localization
    • Nanni, L., & Lumini, A. (2008). Genetic programming for creating Chou's pseudo amino acid based features for submitochondria localization. Amino Acids, 34, 653-660.
    • (2008) Amino Acids , vol.34 , pp. 653-660
    • Nanni, L.1    Lumini, A.2
  • 63
    • 84856475734 scopus 로고    scopus 로고
    • Identifying bacterial virulent proteins by fusing a set of classifiers based on variants of Chou's pseudo amino acid composition and on evolutionary information
    • Nanni, L., Lumini, A., Gupta, D., & Garg, A. (2012). Identifying bacterial virulent proteins by fusing a set of classifiers based on variants of Chou's pseudo amino acid composition and on evolutionary information. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9, 467-475.
    • (2012) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.9 , pp. 467-475
    • Nanni, L.1    Lumini, A.2    Gupta, D.3    Garg, A.4
  • 65
    • 0034791090 scopus 로고    scopus 로고
    • Ubiquitin enters the new millennium
    • Pickart, C. M. (2001). Ubiquitin enters the new millennium. Molecular Cell, 8, 499-504.
    • (2001) Molecular Cell , vol.8 , pp. 499-504
    • Pickart, C.M.1
  • 66
    • 84892958175 scopus 로고    scopus 로고
    • IRSpot-TNCPseAAC: Identify recombination spots with trinucleotide composition and pseudo amino acid components
    • Qiu, W. R., Xiao, X., & Chou, K. C. (2014). iRSpot-TNCPseAAC: Identify recombination spots with trinucleotide composition and pseudo amino acid components. International Journal of Molecular Sciences, 15, 1746-1766.
    • (2014) International Journal of Molecular Sciences , vol.15 , pp. 1746-1766
    • Qiu, W.R.1    Xiao, X.2    Chou, K.C.3
  • 68
    • 33750946999 scopus 로고    scopus 로고
    • Narrative review: Protein degradation and human diseases: The ubiquitin connection
    • Reinstein, E., & Ciechanover, A. (2006). Narrative review: Protein degradation and human diseases: The ubiquitin connection. Annals of Internal Medicine, 145, 676-684.
    • (2006) Annals of Internal Medicine , vol.145 , pp. 676-684
    • Reinstein, E.1    Ciechanover, A.2
  • 69
    • 84984752764 scopus 로고    scopus 로고
    • Assignment of protein function in the postgenomic era
    • Saghatelian, A., & Cravatt, B. F. (2005). Assignment of protein function in the postgenomic era. Nature Chemical Biology, 1, 130-142.
    • (2005) Nature Chemical Biology , vol.1 , pp. 130-142
    • Saghatelian, A.1    Cravatt, B.F.2
  • 70
    • 78649324596 scopus 로고    scopus 로고
    • A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction
    • Sahu, S. S., & Panda, G. (2010). A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. Computational Biology and Chemistry, 34, 320-327.
    • (2010) Computational Biology and Chemistry , vol.34 , pp. 320-327
    • Sahu, S.S.1    Panda, G.2
  • 71
    • 0035878724 scopus 로고    scopus 로고
    • Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    • Schaffer, A. A., Aravind, L., Madden, T. L., Shavirin, S., Spouge, J. L., Wolf, Y. I., ⋯ Altschul, S. F. (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Research, 29, 2994-3005.
    • (2001) Nucleic Acids Research , vol.29 , pp. 2994-3005
    • Schaffer, A.A.1    Aravind, L.2    Madden, T.L.3    Shavirin, S.4    Spouge, J.L.5    Wolf, Y.I.6    Altschul, S.F.7
  • 72
    • 0033016291 scopus 로고    scopus 로고
    • The ubiquitinproteasome pathway and pathogenesis of human diseases
    • Schwartz, A. L., & Ciechanover, A. (1999). The ubiquitinproteasome pathway and pathogenesis of human diseases. Annual Review of Medicine, 50, 57-74.
    • (1999) Annual Review of Medicine , vol.50 , pp. 57-74
    • Schwartz, A.L.1    Ciechanover, A.2
  • 73
    • 37549004451 scopus 로고    scopus 로고
    • PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition
    • Shen, H. B. (2008). PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition. Analytical Biochemistry, 373, 386-388.
    • (2008) Analytical Biochemistry , vol.373 , pp. 386-388
    • Shen, H.B.1
  • 74
    • 69949101944 scopus 로고    scopus 로고
    • A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0
    • Shen, H. B. (2009). A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0. Analytical Biochemistry, 394, 269-274.
    • (2009) Analytical Biochemistry , vol.394 , pp. 269-274
    • Shen, H.B.1
  • 75
    • 77957297596 scopus 로고    scopus 로고
    • Virus-mPLoc: A fusion classifier for viral protein subcellular location prediction by incorporating multiple sites
    • Shen, H. B. (2010). Virus-mPLoc: A fusion classifier for viral protein subcellular location prediction by incorporating multiple sites. Journal of Biomolecular Structure and Dynamics, 28, 175-186.
    • (2010) Journal of Biomolecular Structure and Dynamics , vol.28 , pp. 175-186
    • Shen, H.B.1
  • 76
    • 33748150984 scopus 로고    scopus 로고
    • Fuzzy KNN for predicting membrane protein types from pseudo amino acid composition
    • Shen, H. B., Yang, J., & Chou, K. C. (2006). Fuzzy KNN for predicting membrane protein types from pseudo amino acid composition. Journal of Theoretical Biology, 240, 9-13.
    • (2006) Journal of Theoretical Biology , vol.240 , pp. 9-13
    • Shen, H.B.1    Yang, J.2    Chou, K.C.3
  • 77
    • 2342477917 scopus 로고    scopus 로고
    • The novel functions of ubiquitination in signaling
    • Sun, L., & Chen, Z. J. (2004). The novel functions of ubiquitination in signaling. Current Opinion in Cell Biology, 16, 119-126.
    • (2004) Current Opinion in Cell Biology , vol.16 , pp. 119-126
    • Sun, L.1    Chen, Z.J.2
  • 78
    • 84868109035 scopus 로고    scopus 로고
    • Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform
    • Sun, X. Y., Shi, S. P., Qiu, J. D., Suo, S. B., Huang, S. Y., & Liang, R. P. (2012). Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform. Molecular BioSystems, 8, 3178-3184.
    • (2012) Molecular BioSystems , vol.8 , pp. 3178-3184
    • Sun, X.Y.1    Shi, S.P.2    Qiu, J.D.3    Suo, S.B.4    Huang, S.Y.5    Liang, R.P.6
  • 79
    • 48249145694 scopus 로고    scopus 로고
    • Computational identification of ubiquitylation sites from protein sequences
    • Tung, C. W., & Ho, S. Y. (2008). Computational identification of ubiquitylation sites from protein sequences. BMC Bioinformatics, 9, 310.
    • (2008) BMC Bioinformatics , vol.9 , pp. 310
    • Tung, C.W.1    Ho, S.Y.2
  • 80
    • 0032594959 scopus 로고    scopus 로고
    • An overview of statistical learning theory
    • Vapnik, V. N. (1999). An overview of statistical learning theory. IEEE Transactions on Neural Networks, 10, 988-999.
    • (1999) IEEE Transactions on Neural Networks , vol.10 , pp. 988-999
    • Vapnik, V.N.1
  • 81
    • 84873955239 scopus 로고    scopus 로고
    • GOASVM: A subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition
    • Wan, S., Mak, M. W., & Kung, S. Y. (2013). GOASVM: A subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition. Journal of Theoretical Biology, 323, 40-48.
    • (2013) Journal of Theoretical Biology , vol.323 , pp. 40-48
    • Wan, S.1    Mak, M.W.2    Kung, S.Y.3
  • 84
    • 80755158862 scopus 로고    scopus 로고
    • ILoc-Plant: A multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites
    • Wu, Z. C., Xiao, X., & Chou, K. C. (2011). iLoc-Plant: A multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites. Molecular BioSystems, 7, 3287-3297.
    • (2011) Molecular BioSystems , vol.7 , pp. 3287-3297
    • Wu, Z.C.1    Xiao, X.2    Chou, K.C.3
  • 85
    • 84883143619 scopus 로고    scopus 로고
    • IGPCR-Drug: A web server for predicting interaction between GPCRs and drugs in cellular networking
    • Xiao, X., Min, J. L., & Wang, P. (2013). iGPCR-Drug: A web server for predicting interaction between GPCRs and drugs in cellular networking. PLoS ONE, 8, e72234.
    • (2013) PLoS ONE , vol.8 , pp. e72234
    • Xiao, X.1    Min, J.L.2    Wang, P.3
  • 86
    • 84875074764 scopus 로고    scopus 로고
    • IAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types
    • Xiao, X., Wang, P., Lin, W. Z., & Jia, J. H. (2013). iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types. Analytical Biochemistry, 436, 168-177.
    • (2013) Analytical Biochemistry , vol.436 , pp. 168-177
    • Xiao, X.1    Wang, P.2    Lin, W.Z.3    Jia, J.H.4
  • 87
    • 79959667141 scopus 로고    scopus 로고
    • ILoc-Virus: A multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites
    • Xiao, X., Wu, Z. C., & Chou, K. C. (2011). iLoc-Virus: A multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites. Journal of Theoretical Biology, 284, 42-51.
    • (2011) Journal of Theoretical Biology , vol.284 , pp. 42-51
    • Xiao, X.1    Wu, Z.C.2    Chou, K.C.3
  • 88
    • 84890539710 scopus 로고    scopus 로고
    • Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the general form of Chou's PseAAC
    • Xie, H. L., Fu, L., & Nie, X. D. (2013). Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the general form of Chou's PseAAC. Protein Engineering, Design & Selection, 26, 735-742.
    • (2013) Protein Engineering, Design & Selection , vol.26 , pp. 735-742
    • Xie, H.L.1    Fu, L.2    Nie, X.D.3
  • 89
    • 84873575437 scopus 로고    scopus 로고
    • ISNO-PseAAC: Predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition
    • Xu, Y., Ding, J., & Wu, L. Y. (2013). iSNO-PseAAC: Predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition. PLoS ONE, 8, e55844.
    • (2013) PLoS ONE , vol.8 , pp. e55844
    • Xu, Y.1    Ding, J.2    Wu, L.Y.3
  • 90
    • 84885156363 scopus 로고    scopus 로고
    • ISNO-AAPair: Incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins
    • Xu, Y., Shao, X. J., & Wu, L. Y. (2013). iSNO-AAPair: Incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins. PeerJ, 1, e171.
    • (2013) PeerJ , vol.1 , pp. e171
    • Xu, Y.1    Shao, X.J.2    Wu, L.Y.3
  • 91
    • 84899856397 scopus 로고    scopus 로고
    • IHyd-PseAAC: Predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition
    • Xu, Y., Wen, X., Shao, X. J., & Deng, N. Y. (2014). iHyd-PseAAC: Predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition. International Journal of Molecular Sciences, 15, 7594-7610.
    • (2014) International Journal of Molecular Sciences , vol.15 , pp. 7594-7610
    • Xu, Y.1    Wen, X.2    Shao, X.J.3    Deng, N.Y.4
  • 92
    • 84905982402 scopus 로고    scopus 로고
    • INitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition
    • Xu, Y., Wen, X., Wen, L. S., & Wu, L. Y. (2014). iNitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition. PLoS ONE, 9, e105018.
    • (2014) PLoS ONE , vol.9 , pp. e105018
    • Xu, Y.1    Wen, X.2    Wen, L.S.3    Wu, L.Y.4
  • 93
    • 43149104120 scopus 로고    scopus 로고
    • Using the concept of Chou's pseudo amino acid composition to predict protein subcellular localization: An approach by incorporating evolutionary information and von Neumann entropies
    • Zhang, S. W., Zhang, Y. L., Yang, H. F., Zhao, C. H., & Pan, Q. (2008). Using the concept of Chou's pseudo amino acid composition to predict protein subcellular localization: An approach by incorporating evolutionary information and von Neumann entropies. Amino Acids, 34, 565-572.
    • (2008) Amino Acids , vol.34 , pp. 565-572
    • Zhang, S.W.1    Zhang, Y.L.2    Yang, H.F.3    Zhao, C.H.4    Pan, Q.5
  • 94
    • 84055217653 scopus 로고    scopus 로고
    • Prediction of lysine ubiquitylation with ensemble classifier and feature selection
    • Zhao, X., Li, X., Ma, Z., & Yin, M. (2011). Prediction of lysine ubiquitylation with ensemble classifier and feature selection. International Journal of Molecular Sciences, 12, 8347-8361.
    • (2011) International Journal of Molecular Sciences , vol.12 , pp. 8347-8361
    • Zhao, X.1    Li, X.2    Ma, Z.3    Yin, M.4
  • 95
    • 84865373769 scopus 로고    scopus 로고
    • Identifying GPCRs and their types with Chou's pseudo amino acid composition: An approach from multi-scale energy representation and position specific scoring matrix
    • Zia Ur, R., & Khan, A. (2012). Identifying GPCRs and their types with Chou's pseudo amino acid composition: An approach from multi-scale energy representation and position specific scoring matrix. Protein and Peptide Letters, 19, 890-903.
    • (2012) Protein and Peptide Letters , vol.19 , pp. 890-903
    • Zia Ur, R.1    Khan, A.2
  • 96
    • 78650099168 scopus 로고    scopus 로고
    • Supersecondary structure prediction using Chou's pseudo amino acid composition
    • Zou, D., He, Z., He, J., & Xia, Y. (2011). Supersecondary structure prediction using Chou's pseudo amino acid composition. Journal of Computational Chemistry, 32, 271-278.
    • (2011) Journal of Computational Chemistry , vol.32 , pp. 271-278
    • Zou, D.1    He, Z.2    He, J.3    Xia, Y.4


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