메뉴 건너뛰기




Volumn 9, Issue 9, 2014, Pages

IDNA-Prot|dis: Identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA BINDING PROTEIN;

EID: 84906975785     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0106691     Document Type: Article
Times cited : (287)

References (102)
  • 1
    • 80055101037 scopus 로고    scopus 로고
    • Structural and mutational studies of a hyperthermophilic intein from DNA polymerase II of Pyrococcus abyssi
    • Du Z, Liu J, Albracht CD, Hsu A, Chen W, et al. (2011) Structural and mutational studies of a hyperthermophilic intein from DNA polymerase II of Pyrococcus abyssi. J Biol Chem 286:38638-38648.
    • (2011) J Biol Chem , vol.286 , pp. 38638-38648
    • Du, Z.1    Liu, J.2    Albracht, C.D.3    Hsu, A.4    Chen, W.5
  • 3
    • 4143064791 scopus 로고    scopus 로고
    • Moment-based prediction of DNA-binding proteins
    • Ahmad S, Sarai A (2004) Moment-based Prediction of DNA-binding Proteins. J Mol Biol 341:65-71.
    • (2004) J Mol Biol , vol.341 , pp. 65-71
    • Ahmad, S.1    Sarai, A.2
  • 4
    • 47249125424 scopus 로고    scopus 로고
    • DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions
    • Gao M, Skolnick J (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Research 36:3978-3992.
    • (2008) Nucleic Acids Research , vol.36 , pp. 3978-3992
    • Gao, M.1    Skolnick, J.2
  • 5
    • 73449119593 scopus 로고    scopus 로고
    • A threading-based method for the prediction of DNA-binding proteins with application to the human genome
    • Gao M, Skolnick J (2009) A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome. PLoS Comput Biol 5:e1000567.
    • (2009) PLoS Comput Biol , vol.5 , pp. e1000567
    • Gao, M.1    Skolnick, J.2
  • 6
    • 0038644483 scopus 로고    scopus 로고
    • Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence
    • Cai Y, Lin SL (2003) Support Vector Machines for Predicting rRNA-, RNA-, and DNA-binding Proteins from Amino Acid Sequence. Biochimica et Biophysica Acta (BBA)-Proteins & Proteomics 1648:127-133.
    • (2003) Biochimica et Biophysica Acta (BBA)-proteins & Proteomics , vol.1648 , pp. 127-133
    • Cai, Y.1    Lin, S.L.2
  • 8
    • 38149007012 scopus 로고    scopus 로고
    • Predicting DNA-binding proteins: Approached from Chou's pseudo amino acid composition and other specific sequence features
    • Fang Y, Guo Y, Feng Y, Li M (2008) Predicting DNA-binding Proteins: Approached From Chou's Pseudo Amino Acid Composition and Other Specific Sequence Features. Amino Acids 34:103-109.
    • (2008) Amino Acids , vol.34 , pp. 103-109
    • Fang, Y.1    Guo, Y.2    Feng, Y.3    Li, M.4
  • 9
    • 77953693713 scopus 로고    scopus 로고
    • Boosting the prediction and understanding of dnabinding domains from sequence
    • Langlois RE, Lu H (2010) Boosting the Prediction and Understanding of DNAbinding Domains from Sequence. Nucleic Acids Research 38:3149-3158.
    • (2010) Nucleic Acids Research , vol.38 , pp. 3149-3158
    • Langlois, R.E.1    Lu, H.2
  • 10
    • 84874690054 scopus 로고    scopus 로고
    • An improved sequence based prediction protocol for DNA-binding proteins using svm and comprehensive feature analysis
    • Zou C, Gong J, Li H (2013) An Improved Sequence Based Prediction Protocol for DNA-binding Proteins using SVM and Comprehensive Feature Analysis. BMC Bioinformatics 14:90.
    • (2013) BMC Bioinformatics , vol.14 , pp. 90
    • Zou, C.1    Gong, J.2    Li, H.3
  • 11
    • 61849153473 scopus 로고    scopus 로고
    • A novel computational approach to predict transcription factor DNA binding preference
    • Cai Y, He J, Li X, Lu L, Yang X, et al. (2008) A Novel Computational Approach to Predict Transcription Factor DNA binding Preference. Journal of Proteome Research 8:999-1003.
    • (2008) Journal of Proteome Research , vol.8 , pp. 999-1003
    • Cai, Y.1    He, J.2    Li, X.3    Lu, L.4    Yang, X.5
  • 12
    • 34447293576 scopus 로고    scopus 로고
    • Design of accurate predictors for DNA-binding sites in proteins using hybrid SVM-PSSM method
    • Ho SY, Yu FC, Chang CY, Huang HL (2007) Design of Accurate Predictors for DNA-binding Sites in Proteins Using Hybrid SVM-PSSM Method. BioSystems 90:234-241.
    • (2007) BioSystems , vol.90 , pp. 234-241
    • Ho, S.Y.1    Yu, F.C.2    Chang, C.Y.3    Huang, H.L.4
  • 13
    • 33846803179 scopus 로고    scopus 로고
    • DISPLAR: An accurate method for predicting DNA-binding sites on protein surfaces
    • Tjong H, Zhou HX (2007) DISPLAR: an Accurate Method for Predicting DNA-binding Sites on Protein Surfaces. Nucleic Acids Research 35:1465-1477.
    • (2007) Nucleic Acids Research , vol.35 , pp. 1465-1477
    • Tjong, H.1    Zhou, H.X.2
  • 14
    • 67249090413 scopus 로고    scopus 로고
    • DNA-prot: Identification of DNA binding proteins from protein sequence information using random forest
    • Kumar KK, Pugalenthi G, Suganthan PN (2009) DNA-Prot: Identification of DNA binding Proteins from Protein Sequence Information Using Random Forest. Journal of Biomolecular Structure and Dynamics 26:679-686.
    • (2009) Journal of Biomolecular Structure and Dynamics , vol.26 , pp. 679-686
    • Kumar, K.K.1    Pugalenthi, G.2    Suganthan, P.N.3
  • 15
    • 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
  • 18
    • 84905982402 scopus 로고    scopus 로고
    • INitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition
    • Xu Y, Wen X, Wen LS, Wu LY, Deng NY, et al. (2014) iNitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition. PLoS ONE: http://dx.plos.org/10.1371/journal.pone.0105018.
    • (2014) PLoS ONE
    • Xu, Y.1    Wen, X.2    Wen, L.S.3    Wu, L.Y.4    Deng, N.Y.5
  • 19
    • 84903592187 scopus 로고    scopus 로고
    • ICTX-Type: A sequence-based predictor for identifying the types of conotoxins in targeting ion channels
    • Ding H, Deng EZ, Yuan LF, Liu L, Lin H, et al. (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
  • 20
    • 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 XJ, Deng NY (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
  • 21
    • 84902162941 scopus 로고    scopus 로고
    • IMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach
    • Qiu WR, Xiao X, Lin WZ (2014) iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach. Biomed Res Int 2014:947416.
    • (2014) Biomed Res Int , vol.2014 , pp. 947416
    • Qiu, W.R.1    Xiao, X.2    Lin, W.Z.3
  • 22
    • 84896470341 scopus 로고    scopus 로고
    • INR-Drug: Predicting the interaction of drugs with nuclear receptors in cellular networking
    • Fan YN, Xiao X, Min JL (2014) iNR-Drug: Predicting the interaction of drugs with nuclear receptors in cellular networking. Intenational Journal of Molecular Sciences 15:4915-4937.
    • (2014) Intenational Journal of Molecular Sciences , vol.15 , pp. 4915-4937
    • Fan, Y.N.1    Xiao, X.2    Min, J.L.3
  • 23
    • 84896463976 scopus 로고    scopus 로고
    • INuc-PseKNC: A sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
    • Guo SH, Deng EZ, Xu LQ, Ding H, Lin H, et al. (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
  • 24
    • 84892958175 scopus 로고    scopus 로고
    • IRSpot-TNCPseAAC: Identify recombination spots with trinucleotide composition and pseudo amino acid components
    • Qiu WR, Xiao X (2014) iRSpot-TNCPseAAC: Identify recombination spots with trinucleotide composition and pseudo amino acid components. Int J Mol Sci 15:1746-1766.
    • (2014) Int J Mol Sci , vol.15 , pp. 1746-1766
    • Qiu, W.R.1    Xiao, X.2
  • 25
    • 84921500317 scopus 로고    scopus 로고
    • ITIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudotrinucleotide composition
    • Chen W, Feng PM, Deng EZ (2014) iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudotrinucleotide composition. Analytical Biochemistry: 10.1016/j.ab.2014.1006.1022.
    • (2014) Analytical Biochemistry
    • Chen, W.1    Feng, P.M.2    Deng, E.Z.3
  • 26
    • 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 LY (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
  • 27
    • 79951518208 scopus 로고    scopus 로고
    • Some remarks on protein attribute prediction and pseudo amino acid composition
    • Chou KC (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
  • 28
    • 34548606295 scopus 로고    scopus 로고
    • Review: Recent progresses in protein subcellular location prediction
    • Chou KC, Shen HB (2007) Review: Recent progresses 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
  • 29
    • 23144438711 scopus 로고    scopus 로고
    • PISCES: Recent improvements to a PDB sequence culling server
    • Wang G, Dunbrack RJ (2005) PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res 33:W94-W98.
    • (2005) Nucleic Acids Res , vol.33 , pp. W94-W98
    • Wang, G.1    Dunbrack, R.J.2
  • 30
    • 84868128310 scopus 로고    scopus 로고
    • INuc-PhysChem: A sequence-based predictor for identifying nucleosomes via physicochemical properties
    • Chen W, Lin H, Feng PM, Ding C, Zuo YC, et al. (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    Zuo, Y.C.5
  • 31
    • 23944438427 scopus 로고    scopus 로고
    • Prediction of G-protein-coupled receptor classes
    • Chou KC (2005) Prediction of G-protein-coupled receptor classes. Journal of Proteome Research 4:1413-1418.
    • (2005) Journal of Proteome Research , vol.4 , pp. 1413-1418
    • Chou, K.C.1
  • 34
    • 84876053736 scopus 로고    scopus 로고
    • IRSpot-PseDNC: Identify recombination spots with pseudo dinucleotide composition
    • Chen W, Feng PM, Lin H, Chou KC (2013) iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition Nucleic Acids Research 41:e69.
    • (2013) Nucleic Acids Research , vol.41 , pp. e69
    • Chen, W.1    Feng, P.M.2    Lin, H.3    Chou, K.C.4
  • 35
    • 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, et al. (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
  • 36
    • 78649326452 scopus 로고    scopus 로고
    • AFPPred: A random forest approach for predicting antifreeze proteins from sequence-derived properties
    • Kandaswamy KK, Martinetz T, Moller S, Suganthan PN, et al. (2011) AFPPred: A random forest approach for predicting antifreeze proteins from sequence-derived properties. Journal of Theoretical Biology 270:56-62.
    • (2011) Journal of Theoretical Biology , vol.270 , pp. 56-62
    • Kandaswamy, K.K.1    Martinetz, T.2    Moller, S.3    Suganthan, P.N.4
  • 37
    • 28844434867 scopus 로고    scopus 로고
    • Prediction of protease types in a hybridization space
    • Chou KC, Cai YD (2006) Prediction of protease types in a hybridization space. Biochem Biophys Res Comm 339:1015-1020.
    • (2006) Biochem Biophys Res Comm , vol.339 , pp. 1015-1020
    • Chou, K.C.1    Cai, Y.D.2
  • 38
    • 33747197197 scopus 로고    scopus 로고
    • Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers
    • Chou KC, Shen HB (2006) Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers. Journal of Proteome Research 5:1888-1897.
    • (2006) Journal of Proteome Research , vol.5 , pp. 1888-1897
    • Chou, K.C.1    Shen, H.B.2
  • 39
    • 34249318001 scopus 로고    scopus 로고
    • Euk-mPLoc: A fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites
    • Chou KC, Shen HB (2007) Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. Journal of Proteome Research 6:1728-1734.
    • (2007) Journal of Proteome Research , vol.6 , pp. 1728-1734
    • Chou, K.C.1    Shen, H.B.2
  • 40
    • 69949101944 scopus 로고    scopus 로고
    • A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0
    • Shen HB (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
  • 41
    • 33748150984 scopus 로고    scopus 로고
    • Fuzzy KNN for predicting membrane protein types from pseudo amino acid composition
    • Shen HB, Yang J (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
  • 42
    • 84883143619 scopus 로고    scopus 로고
    • IGPCR-Drug: A web server for predicting interaction between GPCRs and drugs in cellular networking
    • Xiao X, Min JL, 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
  • 43
    • 84877758233 scopus 로고    scopus 로고
    • Some remarks on predicting multi-label attributes in molecular biosystems
    • Chou KC (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
  • 44
    • 12744279642 scopus 로고    scopus 로고
    • Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    • Chou KC (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
  • 45
    • 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 Trans Comput Biol Bioinform 9:467-475.
    • (2012) IEEE/ACM Trans Comput Biol Bioinform , vol.9 , pp. 467-475
    • Nanni, L.1    Lumini, A.2    Gupta, D.3    Garg, A.4
  • 46
    • 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
  • 47
    • 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
  • 48
    • 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 KK, Pugalenthi G, Moller S, Hartmann E, Kalies KU, et al. (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
  • 49
    • 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 YK, Li KB (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
  • 50
    • 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 & Peptide Letters 19:411-421.
    • (2012) Protein & Peptide Letters , vol.19 , pp. 411-421
    • Hayat, M.1    Khan, A.2
  • 51
    • 84896693437 scopus 로고    scopus 로고
    • A short survey on genetic sequences, Chou's pseudo amino acid composition and its combination with fuzzy set theory
    • Georgiou DN, Karakasidis TE, Megaritis AC (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; open access at http://www.benthamscience.com/open/tobioij/articles/V007/SI0025TOBIOIJ/0041TOBIOIJ.pdf.
    • (2013) The Open Bioinformatics Journal , vol.7 , pp. 41-48
    • Georgiou, D.N.1    Karakasidis, T.E.2    Megaritis, A.C.3
  • 52
    • 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 & Peptide Letters 17:1207-1214.
    • (2010) Protein & Peptide Letters , vol.17 , pp. 1207-1214
    • Mohabatkar, H.1
  • 53
    • 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
  • 54
    • 84876370111 scopus 로고    scopus 로고
    • Predicting antibacterial peptides by the concept of Chou's pseudoamino acid composition and machine learning methods
    • Khosravian M, Faramarzi FK, Beigi MM, Behbahani M, Mohabatkar H (2013) Predicting Antibacterial Peptides by the Concept of Chou's Pseudoamino Acid Composition and Machine Learning Methods. Protein & Peptide Letters 20:180-186.
    • (2013) Protein & Peptide Letters , vol.20 , pp. 180-186
    • Khosravian, M.1    Faramarzi, F.K.2    Beigi, M.M.3    Behbahani, M.4    Mohabatkar, H.5
  • 55
    • 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 MM, 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
  • 56
    • 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
    • MohammadBeigi 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
    • MohammadBeigi, M.1    Behjati, M.2    Mohabatkar, H.3
  • 57
    • 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. J Theor Biol 344:12-18.
    • (2014) J Theor Biol , vol.344 , pp. 12-18
    • Kong, L.1    Zhang, L.2    Lv, J.3
  • 58
    • 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 & Peptide Letters 19:890-903.
    • (2012) Protein & Peptide Letters , vol.19 , pp. 890-903
    • Zia Ur, R.1    Khan, A.2
  • 59
    • 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 XY, Shi SP, Qiu JD, Suo SB, Huang SY, et al. (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
  • 60
    • 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
  • 61
    • 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
  • 62
    • 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
  • 63
    • 72449203319 scopus 로고    scopus 로고
    • Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology
    • Chou KC (2009) Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology. Current Proteomics 6:262-274.
    • (2009) Current Proteomics , vol.6 , pp. 262-274
    • Chou, K.C.1
  • 64
    • 84900463301 scopus 로고    scopus 로고
    • PseKNC: A flexible web-server for generating pseudo K-tuple nucleotide composition
    • Chen W, Lei TY, Jin DC (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
  • 65
    • 84859932176 scopus 로고    scopus 로고
    • PseAAC-Builder: A cross-platform standalone 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 standalone 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
  • 66
    • 84875576158 scopus 로고    scopus 로고
    • Propy: A tool to generate various modes of Chou's PseAAC
    • Cao DS, Xu QS, Liang YZ (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
  • 67
    • 79951518208 scopus 로고    scopus 로고
    • Some remarks on protein attribute prediction and pseudo amino acid composition (50th Anniversary Year Review)
    • Chou KC (2011) Some remarks on protein attribute prediction and pseudo amino acid composition (50th Anniversary Year Review). Journal of Theoretical Biology 273:236-247.
    • (2011) Journal of Theoretical Biology , vol.273 , pp. 236-247
    • Chou, K.C.1
  • 68
    • 0029051959 scopus 로고
    • A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space
    • Chou KC (1995) A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Structure, Function & Genetics 21:319-344.
    • (1995) Proteins: Structure, Function & Genetics , vol.21 , pp. 319-344
    • Chou, K.C.1
  • 69
    • 0033406884 scopus 로고    scopus 로고
    • Protein secondary structural content prediction
    • Liu W (1999) Protein secondary structural content prediction. Protein Engineering 12:1041-1050.
    • (1999) Protein Engineering , vol.12 , pp. 1041-1050
    • Liu, W.1
  • 70
    • 0032781417 scopus 로고    scopus 로고
    • Using pair-coupled amino acid composition to predict protein secondary structure content
    • Chou KC (1999) Using pair-coupled amino acid composition to predict protein secondary structure content. Journal of Protein Chemistry 18:473-480.
    • (1999) Journal of Protein Chemistry , vol.18 , pp. 473-480
    • Chou, K.C.1
  • 71
    • 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 XJ, Wu LY (2013) iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins. Peer J 1:e171.
    • (2013) Peer J , vol.1 , pp. e171
    • Xu, Y.1    Shao, X.J.2    Wu, L.Y.3
  • 72
    • 52149087297 scopus 로고    scopus 로고
    • Predicting membrane protein types by the LLDA algorithm
    • Wang T, Yang J, Shen HB (2008) Predicting membrane protein types by the LLDA algorithm. Protein & Peptide Letters 15:915-921.
    • (2008) Protein & Peptide Letters , vol.15 , pp. 915-921
    • Wang, T.1    Yang, J.2    Shen, H.B.3
  • 73
    • 84885640993 scopus 로고    scopus 로고
    • IHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
    • Feng PM, 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
  • 74
    • 65649149743 scopus 로고    scopus 로고
    • Reduced Amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
    • Peterson EL, Kondev J, Theriot JA, Phillips R (2009) Reduced Amino Acid Alphabets Exhibit an Improved Sensitivity and Selectivity in Fold Assignment. Bioinformatics 25:1356-1362.
    • (2009) Bioinformatics , vol.25 , pp. 1356-1362
    • Peterson, E.L.1    Kondev, J.2    Theriot, J.A.3    Phillips, R.4
  • 75
    • 25144470285 scopus 로고    scopus 로고
    • Low-frequency Fourier spectrum for predicting membrane protein types
    • Liu H, Wang M (2005) Low-frequency Fourier spectrum for predicting membrane protein types. Biochem Biophys Res Commun 336:737-739.
    • (2005) Biochem Biophys Res Commun , vol.336 , pp. 737-739
    • Liu, H.1    Wang, M.2
  • 76
    • 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 MW, Kung SY (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
  • 77
    • 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
  • 78
    • 84902186435 scopus 로고    scopus 로고
    • ISS-PseDNC: Identifying splicing sites using pseudo dinucleotide composition
    • Chen W, Feng PM, Lin H (2014) iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition. Biomed Research International 2014:623149.
    • (2014) Biomed Research International , vol.2014 , pp. 623149
    • Chen, W.1    Feng, P.M.2    Lin, H.3
  • 80
    • 0037195776 scopus 로고    scopus 로고
    • Using functional domain composition and support vector machines for prediction of protein subcellular location
    • Chou KC, Cai YD (2002) Using functional domain composition and support vector machines for prediction of protein subcellular location. Journal of Biological Chemistry 277:45765-45769.
    • (2002) Journal of Biological Chemistry , vol.277 , pp. 45765-45769
    • Chou, K.C.1    Cai, Y.D.2
  • 81
    • 0038636605 scopus 로고    scopus 로고
    • Support vector machines for predicting membrane protein types by using functional domain composition
    • Cai YD, Zhou GP (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
  • 84
    • 84899962803 scopus 로고    scopus 로고
    • Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction
    • Mondal S, Pai PP (2014) Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction. J Theor Biol 356:30-35.
    • (2014) J Theor Biol , vol.356 , pp. 30-35
    • Mondal, S.1    Pai, P.P.2
  • 85
    • 84904506417 scopus 로고    scopus 로고
    • Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine
    • Hayat M, Iqbal N (2014) Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine. Comput Methods Programs Biomed.
    • (2014) Comput Methods Programs Biomed.
    • Hayat, M.1    Iqbal, N.2
  • 86
    • 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 SW, Zhang YL, Yang HF, Zhao CH, 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
  • 87
    • 0035030201 scopus 로고    scopus 로고
    • Using subsite coupling to predict signal peptides
    • Chou KC (2001) Using subsite coupling to predict signal peptides. Protein Engineering 14:75-79.
    • (2001) Protein Engineering , vol.14 , pp. 75-79
    • Chou, K.C.1
  • 88
    • 0035748859 scopus 로고    scopus 로고
    • Prediction of signal peptides using scaled window
    • Chou KC (2001) Prediction of signal peptides using scaled window. Peptides 22:1973-1979.
    • (2001) Peptides , vol.22 , pp. 1973-1979
    • Chou, K.C.1
  • 89
    • 84867004398 scopus 로고    scopus 로고
    • Using Amino acid physicochemical distance transformation for fast protein remote homology detection
    • Liu B, Wang X, Chen Q, Dong Q, Lan X (2012) Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection. PLoS One 7:e46633.
    • (2012) PLoS One , vol.7 , pp. e46633
    • Liu, B.1    Wang, X.2    Chen, Q.3    Dong, Q.4    Lan, X.5
  • 90
    • 84873900718 scopus 로고    scopus 로고
    • Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search
    • Szabóová A, Kuželka O, Železní F, Tolar J (2012) Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search. BMC Bioinformatics 13:S3.
    • (2012) BMC Bioinformatics , vol.13 , pp. S3
    • Szabóová, A.1    Kuželka, O.2    Železní, F.3    Tolar, J.4
  • 91
    • 0035803581 scopus 로고    scopus 로고
    • Crystal structure of the CENP-B protein-DNA complex: The DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA
    • Tanaka Y, Nureki O, Kurumizaka H, Fukai S, Kawaguchi S, et al. (2001) Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. EMBO J 20:6612-6618.
    • (2001) EMBO J , vol.20 , pp. 6612-6618
    • Tanaka, Y.1    Nureki, O.2    Kurumizaka, H.3    Fukai, S.4    Kawaguchi, S.5
  • 92
    • 84857411675 scopus 로고    scopus 로고
    • INR-PhysChem: A sequence-based predictor for identifying nuclear receptors and their subfamilies via physical-chemical property matrix
    • Xiao X, Wang P (2012) iNR-PhysChem: A Sequence-Based Predictor for Identifying Nuclear Receptors and Their Subfamilies via Physical-Chemical Property Matrix. PLoS ONE 7:e30869.
    • (2012) PLoS ONE , vol.7 , pp. e30869
    • Xiao, X.1    Wang, P.2
  • 93
    • 0031449933 scopus 로고    scopus 로고
    • Prediction of the tertiary structure and substrate binding site of caspase-8
    • Chou KC, Jones D, Heinrikson RL (1997) Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Letters 419:49-54.
    • (1997) FEBS Letters , vol.419 , pp. 49-54
    • Chou, K.C.1    Jones, D.2    Heinrikson, R.L.3
  • 94
    • 33845467978 scopus 로고    scopus 로고
    • A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets
    • Ogul H, Mumcuoglu EU (2007) A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets. BioSystems 87:75-81.
    • (2007) BioSystems , vol.87 , pp. 75-81
    • Ogul, H.1    Mumcuoglu, E.U.2
  • 95
    • 59449107736 scopus 로고    scopus 로고
    • An ensemble of reduced alphabets with protein encoding based on grouped weight for predicting DNA-binding proteins
    • Nanni L, Lumini A (2009) An Ensemble of Reduced Alphabets with Protein Encoding Based on Grouped Weight for Predicting DNA-binding Proteins. Amino Acids 36:167-175.
    • (2009) Amino Acids , vol.36 , pp. 167-175
    • Nanni, L.1    Lumini, A.2
  • 96
    • 38649127567 scopus 로고    scopus 로고
    • Identification of DNA-binding proteins using support vector machines and evolutionary profiles
    • Kumar M, Gromiha MM, Raghava GP (2007) Identification of DNA-binding Proteins Using Support Vector Machines and Evolutionary Profiles. BMC Bioinformatics 8:463.
    • (2007) BMC Bioinformatics , vol.8 , pp. 463
    • Kumar, M.1    Gromiha, M.M.2    Raghava, G.P.3
  • 97
    • 84899864030 scopus 로고    scopus 로고
    • Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian Naive Bayes
    • Lou W, Wang X, Chen F, Chen Y, Jiang B, et al. (2014) Sequence Based Prediction of DNA-Binding Proteins Based on Hybrid Feature Selection Using Random Forest and Gaussian Naive Bayes. PLoS ONE 9:e86703.
    • (2014) PLoS ONE , vol.9 , pp. e86703
    • Lou, W.1    Wang, X.2    Chen, F.3    Chen, Y.4    Jiang, B.5
  • 98
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Res 25:3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 99
    • 77649339280 scopus 로고    scopus 로고
    • Review: Recent advances in developing web-servers for predicting protein attributes
    • Chou KC, Shen HB (2009) Review: recent advances in developing web-servers for predicting protein attributes. Natural Science 2:63-92: open access at http://dx.doi.org/10.4236/ns.2009.12011
    • (2009) Natural Science , vol.2 , pp. 63-92
    • Chou, K.C.1    Shen, H.B.2
  • 100
    • 84893021381 scopus 로고    scopus 로고
    • IEzy-drug: A web server for identifying the interaction between enzymes and drugs in cellular networking
    • Min JL, Xiao X (2013) iEzy-Drug: A web server for identifying the interaction between enzymes and drugs in cellular networking. BioMed Research International 2013:701317.
    • (2013) BioMed Research International , vol.2013 , pp. 701317
    • Min, J.L.1    Xiao, X.2
  • 101
    • 84883661549 scopus 로고    scopus 로고
    • ICDI-PseFpt: Identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints
    • Xiao X, Min JL, Wang P (2013) iCDI-PseFpt: Identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints. Journal of Theoretical Biology 337 C: 71-79.
    • (2013) Journal of Theoretical Biology , vol.337 C , pp. 71-79
    • Xiao, X.1    Min, J.L.2    Wang, P.3
  • 102
    • 33646067733 scopus 로고    scopus 로고
    • Efficient prediction of nucleic acid binding function from low-resolution protein structures
    • Szilagyi A, Skolnick J (2006) Efficient Prediction of Nucleic Acid Binding Function from Low-resolution Protein Structures. J Mol Biol 358:922-933.
    • (2006) J Mol Biol , vol.358 , pp. 922-933
    • Szilagyi, A.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.