메뉴 건너뛰기




Volumn 7, Issue , 2017, Pages

Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chou's general PseAAC

Author keywords

[No Author keywords available]

Indexed keywords

ANTIFUNGAL AGENT; ANTIMICROBIAL CATIONIC PEPTIDE; ANTIVIRUS AGENT;

EID: 85012302320     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep42362     Document Type: Article
Times cited : (357)

References (51)
  • 1
    • 35448929949 scopus 로고    scopus 로고
    • Analysis and prediction of antibacterial peptides
    • Lata, S., Sharma, B. K., Raghava, G. P. S. Analysis and prediction of antibacterial peptides. BMC Bioinform. 8, 263 (2007).
    • (2007) BMC Bioinform. , vol.8 , pp. 263
    • Lata, S.1    Sharma, B.K.2    Raghava, G.P.S.3
  • 2
    • 84866280179 scopus 로고    scopus 로고
    • In silico identification of novel hevein-like peptide precursors
    • Porto, W. F., Souza, V. A., Nolasco, D. O., Franco, O. L. In silico identification of novel hevein-like peptide precursors. Peptides. 38, 127-136 (2012).
    • (2012) Peptides. , vol.38 , pp. 127-136
    • Porto, W.F.1    Souza, V.A.2    Nolasco, D.O.3    Franco, O.L.4
  • 3
    • 0037371597 scopus 로고    scopus 로고
    • Mechanisms of antimicrobial peptide action and resistance
    • Yeaman, M. R., Yount, N. Y. Mechanisms of antimicrobial peptide action and resistance. Pharmacol. 55, 27-55 (2003).
    • (2003) Pharmacol. , vol.55 , pp. 27-55
    • Yeaman, M.R.1    Yount, N.Y.2
  • 4
    • 14544282377 scopus 로고    scopus 로고
    • Antimicrobial peptides: Pore formers or metabolic inhibitors in bacteria
    • Brogden, K. A. Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria Nat. Rev. Microbiol. 3, 238-250 (2005).
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 238-250
    • Brogden, K.A.1
  • 6
    • 33748413776 scopus 로고    scopus 로고
    • Antibacterial peptides for therapeutic use: Obstacles and realistic outlook
    • Marr, A. K., Gooderham, W. J., Hancock, R. E. W. Antibacterial peptides for therapeutic use: obstacles and realistic outlook. Curr. Opin. Pharmacol. 6, 468-472 (2006).
    • (2006) Curr. Opin. Pharmacol. , vol.6 , pp. 468-472
    • Marr, A.K.1    Gooderham, W.J.2    Hancock, R.E.W.3
  • 7
    • 84875074764 scopus 로고    scopus 로고
    • IAMP-2L: A two-level multi-labe classifier for identifying antimicrobial peptides and their functional types
    • Xiao, X., Wang, P., Lin, W. Z., Jia, J. H., Chou, K. C. iAMP-2L: A two-level multi-labe classifier for identifying antimicrobial peptides and their functional types. Anal. Biochem. 436(2), 168-177 (2013).
    • (2013) Anal. Biochem. , vol.436 , Issue.2 , pp. 168-177
    • Xiao, X.1    Wang, P.2    Lin, W.Z.3    Jia, J.H.4    Chou, K.C.5
  • 8
    • 34249858459 scopus 로고    scopus 로고
    • AMPer: A database and an automated discovery tool for antimicrobial peptides
    • Fjell, C. D., Hancock, R. E., Cherkasov, A. AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinform. 23(9), 1148-1155 (2007).
    • (2007) Bioinform. , vol.23 , Issue.9 , pp. 1148-1155
    • Fjell, C.D.1    Hancock, R.E.2    Cherkasov, A.3
  • 9
    • 75149184631 scopus 로고    scopus 로고
    • AntiBP2: Improved version of antibacterial peptide prediction
    • Lata, S., Mishra, N. K., Raghava, G. P. S. AntiBP2: improved version of antibacterial peptide prediction. BMC Bioinform. 11 (Suppl 1), S19 (2010).
    • (2010) BMC Bioinform. , vol.11 , pp. S19
    • Lata, S.1    Mishra, N.K.2    Raghava, G.P.S.3
  • 10
    • 84864447533 scopus 로고    scopus 로고
    • AVPpred: Collection and prediction of highly effective antiviral peptides
    • Thakur, N., Qureshi, A., Kumar, M. AVPpred: collection and prediction of highly effective antiviral peptides. Nucl. Acids. Res. 40, W199-204 (2012).
    • (2012) Nucl. Acids. Res. , vol.40 , pp. W199-204
    • Thakur, N.1    Qureshi, A.2    Kumar, M.3
  • 12
    • 85027078579 scopus 로고    scopus 로고
    • Improving recognition of antimicrobial peptides and target selectivity through machine learning and genetic programming
    • Veltri, D., Shehu, A., Kamath, U. Improving recognition of antimicrobial peptides and target selectivity through machine learning and genetic programming. IEEE/ACM Trans. Comput. Biol. Bioinform. x(x) (2015).
    • (2015) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.10 , Issue.10
    • Veltri, D.1    Shehu, A.2    Kamath, U.3
  • 16
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein cellular attributes using pseudo amino acid composition
    • Chou, K. C. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins. 43, 246-255 (2001).
    • (2001) Proteins. , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 17
    • 84962865637 scopus 로고    scopus 로고
    • IACP: A sequence-based tool for identifying anticancer peptides
    • Chen, W., Ding, H., Feng, P. iACP: a sequence-based tool for identifying anticancer peptides. Oncotarget. 7, 16895-16909 (2016).
    • (2016) Oncotarget. , vol.7 , pp. 16895-16909
    • Chen, W.1    Ding, H.2    Feng, P.3
  • 18
    • 84957073578 scopus 로고    scopus 로고
    • PSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach
    • Jia, J., Liu, Z., Xiao, X. pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach. J. Theor. Biol. 394, 223-230 (2016).
    • (2016) J. Theor. Biol. , vol.394 , pp. 223-230
    • Jia, J.1    Liu, Z.2    Xiao, X.3
  • 19
    • 84973637727 scopus 로고    scopus 로고
    • ICar-PseCp: Identify carbonylation sites in proteins by Monto Carlo sampling and incorporating sequence coupled effects into general PseAAC
    • Jia, J., Liu, Z., Xiao, X. iCar-PseCp: identify carbonylation sites in proteins by Monto Carlo sampling and incorporating sequence coupled effects into general PseAAC. Oncotarget 7, 34558-34570 (2016a).
    • (2016) Oncotarget , vol.7 , pp. 34558-34570
    • Jia, J.1    Liu, Z.2    Xiao, X.3
  • 20
    • 84983353017 scopus 로고    scopus 로고
    • IDHS-EL: Identifying DNase i hypersensi-tivesites by fusing three different modes of pseudo nucleotide composition into an en-semble learning framework
    • Liu, B., Long, R. iDHS-EL: Identifying DNase I hypersensi-tivesites by fusing three different modes of pseudo nucleotide composition into an en-semble learning framework. Bioinform. 32, 2411-2418 (2016).
    • (2016) Bioinform. , vol.32 , pp. 2411-2418
    • Liu, B.1    Long, R.2
  • 21
    • 84956829573 scopus 로고    scopus 로고
    • PRNAm-PC: Predicting N-methyl-adenosine sites in RNA sequences via physical-chemical properties
    • Liu, Z., Xiao, X., Yu, D. J. pRNAm-PC: Predicting N-methyl-adenosine sites in RNA sequences via physical-chemical properties. Anal. Biochem. 497, 60-67 (2016).
    • (2016) Anal. Biochem. , vol.497 , pp. 60-67
    • Liu, Z.1    Xiao, X.2    Yu, D.J.3
  • 22
    • 84995428311 scopus 로고    scopus 로고
    • IPTM-mLys: Identifying multiple lysine PTM sites and their different types
    • Qiu, W. R., Sun, B. Q., Xiao, X. iPTM-mLys: identifying multiple lysine PTM sites and their different types. Bioinform. 32, 3116-3123 (2016).
    • (2016) Bioinform. , vol.32 , pp. 3116-3123
    • Qiu, W.R.1    Sun, B.Q.2    Xiao, X.3
  • 23
    • 79951518208 scopus 로고    scopus 로고
    • Some remarks on protein attribute prediction and pseudo amino acid composition (50th Anniversary Year Review)
    • Chou, K. C. Some remarks on protein attribute prediction and pseudo amino acid composition (50th Anniversary Year Review). J. Theor. Biol. 273, 236-247 (2011).
    • (2011) J. Theor. Biol. , vol.273 , pp. 236-247
    • Chou, K.C.1
  • 24
    • 84979498105 scopus 로고    scopus 로고
    • APD3: The antimicrobial peptide database as a tool for research and education
    • Wang, G., Li, X., Wang, Z. APD3: the antimicrobial peptide database as a tool for research and education. Nucl. Acids Res. 44(D1), D1087-1093 (2016).
    • (2016) Nucl. Acids Res. , vol.44 , Issue.D1 , pp. D1087-1093
    • Wang, G.1    Li, X.2    Wang, Z.3
  • 25
    • 84879184644 scopus 로고    scopus 로고
    • LAMP: A database linking antimicrobial peptides
    • Zhao, X., Wu, H., Lu, H., Li, G., Huang, Q. LAMP: A database linking antimicrobial peptides. PLoS ONE. 8(6), e66557 (2013).
    • (2013) PLoS ONE. , vol.8 , Issue.6 , pp. e66557
    • Zhao, X.1    Wu, H.2    Lu, H.3    Li, G.4    Huang, Q.5
  • 26
    • 79954616130 scopus 로고    scopus 로고
    • Prediction of antimicrobial peptides based on sequence alignment and feature selection methods
    • Wang, et al. Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS ONE. 6(4), e18476 (2011).
    • (2011) PLoS ONE. , vol.6 , Issue.4 , pp. e18476
    • Wang1
  • 27
    • 84934767390 scopus 로고    scopus 로고
    • Peptides: A package for data mining of antimicrobial peptides
    • Osorio, D., Rondon-Villarreal, P., Torres, R. Peptides: A package for data mining of antimicrobial peptides. The R Journal. 7(1), 4-14 (2015).
    • (2015) The R Journal. , vol.7 , Issue.1 , pp. 4-14
    • Osorio, D.1    Rondon-Villarreal, P.2    Torres, R.3
  • 28
    • 84965039431 scopus 로고    scopus 로고
    • R Development Core Team R foundation for statistical computing, Vienna, Austria
    • R Development Core Team. R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria, 2012. ISBN 3-900051-07-0, http://www.R-project.org
    • (2012) R: A Language and Environment for Statistical Computing
  • 29
    • 5044235541 scopus 로고    scopus 로고
    • Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
    • Fernandez-Escamilla, A. M., Rousseau, F., Schymkowitz, J., Serrano, L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat. Biotech. 22(10), 1302-1306 (2004).
    • (2004) Nat. Biotech. , vol.22 , Issue.10 , pp. 1302-1306
    • Fernandez-Escamilla, A.M.1    Rousseau, F.2    Schymkowitz, J.3    Serrano, L.4
  • 30
    • 84855164403 scopus 로고    scopus 로고
    • AMPA: An automated web server for prediction of protein antimicrobial regions
    • Torrent, et al. AMPA: An automated web server for prediction of protein antimicrobial regions. Bioinform. 28(1), 130-131 (2011).
    • (2011) Bioinform. , vol.28 , Issue.1 , pp. 130-131
    • Torrent1
  • 31
    • 67349192921 scopus 로고    scopus 로고
    • Open-source machine learning: R meets Weka
    • Hornik, K., Buchta, C., Zeileis, A. Open-source machine learning: R meets Weka. Comput. Stat. 24(2), 225-232 (2009).
    • (2009) Comput. Stat. , vol.24 , Issue.2 , pp. 225-232
    • Hornik, K.1    Buchta, C.2    Zeileis, A.3
  • 32
    • 33845703344 scopus 로고    scopus 로고
    • What is a support vector machine
    • Noble, W. S. What is a support vector machine Nat. Biotech. 24(12), 1565-1567 (2006).
    • (2006) Nat. Biotech. , vol.24 , Issue.12 , pp. 1565-1567
    • Noble, W.S.1
  • 33
    • 84924598117 scopus 로고    scopus 로고
    • Prediction of antimicrobial peptides based on sequence alignment and support vector machine-pairwise algorithm utilizing LZ-complexity
    • Ng, N. X., Rosdi, B. A., Shahrudin, S. Prediction of antimicrobial peptides based on sequence alignment and support vector machine-pairwise algorithm utilizing LZ-complexity. BioMed Res. Int. http://dx.doi.org/10.1155/2015/212715 2015.
    • (2015) BioMed Res. Int.
    • Ng, N.X.1    Rosdi, B.A.2    Shahrudin, S.3
  • 35
    • 84876053736 scopus 로고    scopus 로고
    • IRSpot-PseDNC: Identify recombination spots with pseudo dinucleotide composition
    • Chen, W., Feng, P. M., Lin, H. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucl. Acids Res. 41, e68 (2013).
    • (2013) Nucl. Acids Res. , vol.41 , pp. e68
    • Chen, W.1    Feng, P.M.2    Lin, H.3
  • 36
    • 0036889995 scopus 로고    scopus 로고
    • Review: Prediction of protein signal sequences
    • Chou, K. C. Review: Prediction of protein signal sequences. Curr. Protein Pept. Sci. 3, 615-622 (2002).
    • (2002) Curr. Protein Pept. Sci. , vol.3 , pp. 615-622
    • Chou, K.C.1
  • 37
    • 84995377061 scopus 로고    scopus 로고
    • PSumo-CD: Predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC
    • Jia, J., Zhang, L., Liu, Z. pSumo-CD: Predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC. Bioinform. 32, 3133-3141 (2016b).
    • (2016) Bioinform. , vol.32 , pp. 3133-3141
    • Jia, J.1    Zhang, L.2    Liu, Z.3
  • 38
    • 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. Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. Bioinform. 30, 472-479 (2014).
    • (2014) Bioinform. , vol.30 , pp. 472-479
    • Liu, B.1    Zhang, D.2    Xu, R.3
  • 39
    • 84941040066 scopus 로고    scopus 로고
    • IPro54-PseKNC: A sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition
    • Lin, H., Deng, E. Z., Ding, H. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. Nucl. Acids Res. 42, 12961-12972 (2014).
    • (2014) Nucl. Acids Res. , vol.42 , pp. 12961-12972
    • Lin, H.1    Deng, E.Z.2    Ding, H.3
  • 40
    • 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. iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Bioinform. 30, 1522-1529 (2014).
    • (2014) Bioinform. , vol.30 , pp. 1522-1529
    • Guo, S.H.1    Deng, E.Z.2    Xu, L.Q.3
  • 41
    • 84962263478 scopus 로고    scopus 로고
    • IEnhancer-2L: A two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition
    • Liu, B., Fang, L., Long, R. iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. Bioinform. 32, 362-369 (2016a).
    • (2016) Bioinform. , vol.32 , pp. 362-369
    • Liu, B.1    Fang, L.2    Long, R.3
  • 42
    • 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. iLoc-Animal: A multi-label learning classifier for predicting subcellular localization of animal proteins. Mol. Biosyst. 9, 634-644 (2013).
    • (2013) Mol. Biosyst. , vol.9 , pp. 634-644
    • Lin, W.Z.1    Fang, J.A.2    Xiao, X.3
  • 43
    • 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. iLoc-Plant: a multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites. Mol. Biosyst. 7, 3287-3297 (2011).
    • (2011) Mol. Biosyst. , vol.7 , pp. 3287-3297
    • Wu, Z.C.1    Xiao, X.2
  • 44
    • 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. iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types. Anal. Biochem. 436, 168-177 (2013).
    • (2013) Anal. Biochem. , vol.436 , pp. 168-177
    • Xiao, X.1    Wang, P.2    Lin, W.Z.3
  • 45
    • 85019819062 scopus 로고    scopus 로고
    • IATC-mISF: A multi-label classifier for predicting the classes of anatomical therapeutic chemicals
    • Cheng, X., Zhao, S. G., Xiao, X. iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals. Bioinform. 2016, doi: 10.1093/bioinformatics/btw644.
    • (2016) Bioinform.
    • Cheng, X.1    Zhao, S.G.2    Xiao, X.3
  • 46
    • 84877758233 scopus 로고    scopus 로고
    • Some remarks on predicting multi-label attributes in molecular biosystems
    • Chou, K. C. Some remarks on predicting multi-label attributes in molecular biosystems. Mol. Biosyst. 9, 1092-1100 (2013).
    • (2013) Mol. Biosyst. , vol.9 , pp. 1092-1100
    • Chou, K.C.1
  • 47
    • 84940543452 scopus 로고    scopus 로고
    • A statistical approach for 5 splice site prediction using short sequence motif and without encoding sequence data
    • Meher, P. K., Sahu, T. K., Rao, A. R., Wahi, S. D. A statistical approach for 5 splice site prediction using short sequence motif and without encoding sequence data. BMC Bioinform. 15, 362 (2014).
    • (2014) BMC Bioinform. , vol.15 , pp. 362
    • Meher, P.K.1    Sahu, T.K.2    Rao, A.R.3    Wahi, S.D.4
  • 48
    • 0030810993 scopus 로고
    • Finding genes in DNA with a hidden Markov model
    • Henderson, J., Salzberg, S., Fasman, K. H. Finding genes in DNA with a hidden Markov model. J.Comput. Biol. 4, 127-141 (1992).
    • (1992) J.Comput. Biol. , vol.4 , pp. 127-141
    • Henderson, J.1    Salzberg, S.2    Fasman, K.H.3
  • 49
    • 78149315656 scopus 로고    scopus 로고
    • Using rule sets to maximize ROC performance
    • Fawcett, T. Using rule sets to maximize ROC performance., Proc. Int'l Conf. Data Mining. 131-138 (2006).
    • (2006) Proc. Int'l Conf. Data Mining. , pp. 131-138
    • Fawcett, T.1
  • 51
    • 1942451938 scopus 로고    scopus 로고
    • Feature selection for high-dimensional data: A fast correlation-based filter solution
    • Yu, L., Liu, H. Feature selection for high-dimensional data: A fast correlation-based filter solution. In ICML. 3, 856-863 (2003).
    • (2003) ICML , vol.3 , pp. 856-863
    • Yu, L.1    Liu, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.