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Volumn 264, Issue 4, 2010, Pages 1159-1168

Global and local prediction of protein folding rates based on sequence autocorrelation information

Author keywords

Amino acid sequence autocorrelation; Genetic algorithm; Local lazy regression; Multiple linear regression; Protein folding rate

Indexed keywords

AMINO ACID; AUTOCORRELATION; GENETIC ALGORITHM; MOLECULAR ANALYSIS; MULTIPLE REGRESSION; PROTEIN;

EID: 77952953441     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.03.042     Document Type: Article
Times cited : (9)

References (82)
  • 1
    • 0002676017 scopus 로고    scopus 로고
    • Lazy learning: special issue editorial
    • Lazy learning: special issue editorial. Artif. Intell. Rev. 1997, 7-10.
    • (1997) Artif. Intell. Rev. , pp. 7-10
  • 4
    • 85004911383 scopus 로고
    • Positional flexibilities of amino acid residues in globular proteins
    • Bhaskaran P., Ponnuswamy P.K. Positional flexibilities of amino acid residues in globular proteins. Int. J. Peptide Protein Res. 1988, 32:241-255.
    • (1988) Int. J. Peptide Protein Res. , vol.32 , pp. 241-255
    • Bhaskaran, P.1    Ponnuswamy, P.K.2
  • 6
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • Bock J.R., Gough D.A. Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17:455-460.
    • (2001) Bioinformatics , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 7
    • 0021349111 scopus 로고
    • Molecular structures: perception, autocorrelation descriptor and SAR studies
    • Broto P., Moreau G., Vandicke C. Molecular structures: perception, autocorrelation descriptor and SAR studies. Eur. J. Med. Chem. 1984, 19:71-78.
    • (1984) Eur. J. Med. Chem. , vol.19 , pp. 71-78
    • Broto, P.1    Moreau, G.2    Vandicke, C.3
  • 8
    • 34250845013 scopus 로고    scopus 로고
    • Proteometric study of ghrelin receptor function variations upon mutations using amino acid sequence autocorrelation vectors and genetic algorithm-based least square support vector machines
    • Caballero J., Fernández L., Garriga M., Abreu J.I., Collina S., Fernández M. Proteometric study of ghrelin receptor function variations upon mutations using amino acid sequence autocorrelation vectors and genetic algorithm-based least square support vector machines. J. Mol. Graph. Model. 2007, 26:166-178.
    • (2007) J. Mol. Graph. Model. , vol.26 , pp. 166-178
    • Caballero, J.1    Fernández, L.2    Garriga, M.3    Abreu, J.I.4    Collina, S.5    Fernández, M.6
  • 9
    • 33846630833 scopus 로고    scopus 로고
    • SODOCK: swarm optimization for highly flexible protein-ligand docking
    • Chen H.M., Liu B.F., Huang H.L., Hwang S.E., Ho S.I. SODOCK: swarm optimization for highly flexible protein-ligand docking. J. Comput. Chem. 2007, 28:612-623.
    • (2007) J. Comput. Chem. , vol.28 , pp. 612-623
    • Chen, H.M.1    Liu, B.F.2    Huang, H.L.3    Hwang, S.E.4    Ho, S.I.5
  • 10
    • 0034687538 scopus 로고    scopus 로고
    • Prediction of protein subcellular locations by incorporating quasi-sequence-order effect
    • Chou K.C. Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochem. Biophys. Res. Commun. 2000, 278:477-483.
    • (2000) Biochem. Biophys. Res. Commun. , vol.278 , pp. 477-483
    • Chou, K.C.1
  • 11
    • 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 2001, 43:246-255.
    • (2001) Proteins , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 12
    • 12744279642 scopus 로고    scopus 로고
    • Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    • Chou K.C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 2005, 21:10-19.
    • (2005) Bioinformatics , vol.21 , pp. 10-19
    • Chou, K.C.1
  • 13
    • 18344391868 scopus 로고    scopus 로고
    • Prediction of membrane protein types by incorporating amphipathic effects
    • Chou K.C., Cai Y.D. Prediction of membrane protein types by incorporating amphipathic effects. J. Chem. Inf. Model. 2005, 45:407-413.
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 407-413
    • Chou, K.C.1    Cai, Y.D.2
  • 14
    • 45549110576 scopus 로고
    • Regression by local fitting: methods, properties, and computational algorithms
    • Cleveland W.S., Devlin S.J., Grosse E. Regression by local fitting: methods, properties, and computational algorithms. J Econometrics 1988, 37:87-114.
    • (1988) J Econometrics , vol.37 , pp. 87-114
    • Cleveland, W.S.1    Devlin, S.J.2    Grosse, E.3
  • 15
    • 0023972269 scopus 로고
    • Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities
    • David S.H. Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities. Biopolymers 1988, 27:451-477.
    • (1988) Biopolymers , vol.27 , pp. 451-477
    • David, S.H.1
  • 16
    • 0033521194 scopus 로고    scopus 로고
    • First principles prediction of protein folding rates
    • Debe D.A., Goddard W.A. First principles prediction of protein folding rates. J. Mol. Biol. 1999, 294:619-625.
    • (1999) J. Mol. Biol. , vol.294 , pp. 619-625
    • Debe, D.A.1    Goddard, W.A.2
  • 17
    • 0035173844 scopus 로고    scopus 로고
    • The roles of stability and contact order in determining protein folding rates
    • Dinner A.R., Karplus M. The roles of stability and contact order in determining protein folding rates. Nat. Struct. Biol. 2001, 8:21-22.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 21-22
    • Dinner, A.R.1    Karplus, M.2
  • 19
    • 3343000049 scopus 로고    scopus 로고
    • Methods to study protein folding by stopped-flow FT-IR
    • Fabian H., Naumann D. Methods to study protein folding by stopped-flow FT-IR. Methods 2004, 34:28-40.
    • (2004) Methods , vol.34 , pp. 28-40
    • Fabian, H.1    Naumann, D.2
  • 21
    • 0038440629 scopus 로고    scopus 로고
    • A measure of conformational entropy change during thermal protein unfolding using neutron spectroscopy
    • Fitter J. A measure of conformational entropy change during thermal protein unfolding using neutron spectroscopy. Biophys. J. 2003, 84:3924-3930.
    • (2003) Biophys. J. , vol.84 , pp. 3924-3930
    • Fitter, J.1
  • 22
    • 0037402639 scopus 로고    scopus 로고
    • Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics
    • Galzitskaya O.V., Garbuzynskiy S.O., Ivankov D.N., Finkelstein A.V. Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Proteins 2003, 51:162-166.
    • (2003) Proteins , vol.51 , pp. 162-166
    • Galzitskaya, O.V.1    Garbuzynskiy, S.O.2    Ivankov, D.N.3    Finkelstein, A.V.4
  • 23
    • 0037432567 scopus 로고    scopus 로고
    • Local secondary structure content predicts folding rates for simple, two-state proteins
    • Gong H., Isom D.G., Srinivasan R., Rose G.D. Local secondary structure content predicts folding rates for simple, two-state proteins. J. Mol. Biol. 2003, 327:1149-1154.
    • (2003) J. Mol. Biol. , vol.327 , pp. 1149-1154
    • Gong, H.1    Isom, D.G.2    Srinivasan, R.3    Rose, G.D.4
  • 24
    • 0037432567 scopus 로고    scopus 로고
    • Local secondary structure content predicts folding rates for simple, two-state proteins
    • Gong H., Isom D.G., Srinivasan R., Rose G.D. Local secondary structure content predicts folding rates for simple, two-state proteins. J. Mol. Biol. 2003, 327:1149-1154.
    • (2003) J. Mol. Biol. , vol.327 , pp. 1149-1154
    • Gong, H.1    Isom, D.G.2    Srinivasan, R.3    Rose, G.D.4
  • 25
    • 0141959709 scopus 로고    scopus 로고
    • Importance of native-state topology for determining the folding rate of two-state proteins
    • Gromiha M.M. Importance of native-state topology for determining the folding rate of two-state proteins. J. Chem. Inf. Comput. Sci. 2003, 43:1481-1485.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 1481-1485
    • Gromiha, M.M.1
  • 26
    • 18344371857 scopus 로고    scopus 로고
    • A statistical model for predicting protein folding rates from amino acid sequence with structural class information
    • Gromiha M.M. A statistical model for predicting protein folding rates from amino acid sequence with structural class information. J. Chem. Inf. Model. 2005, 45:494-501.
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 494-501
    • Gromiha, M.M.1
  • 27
    • 66149112049 scopus 로고    scopus 로고
    • Multiple contact network is a key determinant to protein folding rates
    • Gromiha M.M. Multiple contact network is a key determinant to protein folding rates. J. Chem. Inf. Model. 2009, 49:1130-1135.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1130-1135
    • Gromiha, M.M.1
  • 28
    • 0035967862 scopus 로고    scopus 로고
    • Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction
    • Gromiha M.M., Selvaraj S. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J. Mol. Biol. 2001, 310:27-32.
    • (2001) J. Mol. Biol. , vol.310 , pp. 27-32
    • Gromiha, M.M.1    Selvaraj, S.2
  • 29
    • 1842464687 scopus 로고    scopus 로고
    • Inter-residue interactions in protein folding and stability
    • Gromiha M.M., Selvaraj S. Inter-residue interactions in protein folding and stability. Prog. Biophys. Mol. Biol. 2004, 86:235-277.
    • (2004) Prog. Biophys. Mol. Biol. , vol.86 , pp. 235-277
    • Gromiha, M.M.1    Selvaraj, S.2
  • 30
    • 38949121906 scopus 로고    scopus 로고
    • Bioinformatics approaches for understanding and predicting protein folding rates
    • Gromiha M.M., Selvaraj S. Bioinformatics approaches for understanding and predicting protein folding rates. Curr. Bioinformatics 2008, 3:1-9.
    • (2008) Curr. Bioinformatics , vol.3 , pp. 1-9
    • Gromiha, M.M.1    Selvaraj, S.2
  • 31
    • 33747822326 scopus 로고    scopus 로고
    • FOLD-RATE: prediction of protein folding rates from amino acid sequence
    • Gromiha M.M., Thangakani A.M., Selvaraj S. FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acids Res. 2006, 34:W70-W74.
    • (2006) Nucleic Acids Res. , vol.34
    • Gromiha, M.M.1    Thangakani, A.M.2    Selvaraj, S.3
  • 32
    • 28544451206 scopus 로고    scopus 로고
    • Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A*0201
    • Guan P., Doytchinova I.A., Walshe V.A., Borrow P., Flower D.R. Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A*0201. J. Med. Chem. 2005, 48:7418-7425.
    • (2005) J. Med. Chem. , vol.48 , pp. 7418-7425
    • Guan, P.1    Doytchinova, I.A.2    Walshe, V.A.3    Borrow, P.4    Flower, D.R.5
  • 33
    • 33746928751 scopus 로고    scopus 로고
    • Local lazy regression: making use of the neighborhood to improve QSAR predictions
    • Guha R., Dutta D., Jurs P.C., Chen T. Local lazy regression: making use of the neighborhood to improve QSAR predictions. J. Chem. Inf. Model. 2006, 46:1836-1847.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1836-1847
    • Guha, R.1    Dutta, D.2    Jurs, P.C.3    Chen, T.4
  • 34
    • 33947600314 scopus 로고    scopus 로고
    • Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness
    • Han L.Y., Zheng C.J., Xie B., Jia J., Ma X.H., Zhu F., Lin H.H., Chen X., Chen Y.Z. Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness. Drug Discov. Today 2007, 12:304-313.
    • (2007) Drug Discov. Today , vol.12 , pp. 304-313
    • Han, L.Y.1    Zheng, C.J.2    Xie, B.3    Jia, J.4    Ma, X.H.5    Zhu, F.6    Lin, H.H.7    Chen, X.8    Chen, Y.Z.9
  • 35
    • 37649004604 scopus 로고    scopus 로고
    • Application of quantum topological molecular similarity descriptors in QSPR study of the O-methylation of substituted phenols
    • Hemmateenejad B., Mohajeri A. Application of quantum topological molecular similarity descriptors in QSPR study of the O-methylation of substituted phenols. J. Comput. Chem. 2008, 29:266-274.
    • (2008) J. Comput. Chem. , vol.29 , pp. 266-274
    • Hemmateenejad, B.1    Mohajeri, A.2
  • 36
    • 0033191625 scopus 로고    scopus 로고
    • Applications of genetic algorithms on the structure-activity relationship analysis of some cinnamamides
    • Hou T.J., Wang J.M., Liao N., Xu X.J. Applications of genetic algorithms on the structure-activity relationship analysis of some cinnamamides. J. Chem. Inf. Comput. Sci. 1999, 39:775-781.
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 775-781
    • Hou, T.J.1    Wang, J.M.2    Liao, N.3    Xu, X.J.4
  • 37
    • 77952957389 scopus 로고    scopus 로고
    • .
  • 38
    • 33646028225 scopus 로고    scopus 로고
    • Amino acid sequence predicts folding rate for middle-size two-state proteins
    • Huang J.T., Tian J. Amino acid sequence predicts folding rate for middle-size two-state proteins. Proteins 2006, 63:551-554.
    • (2006) Proteins , vol.63 , pp. 551-554
    • Huang, J.T.1    Tian, J.2
  • 39
    • 46449092464 scopus 로고    scopus 로고
    • Analysis and prediction of protein folding rates using quadratic response surface models
    • Huang L.T., Gromiha M.M. Analysis and prediction of protein folding rates using quadratic response surface models. J. Comput. Chem. 2008, 29:1675-1683.
    • (2008) J. Comput. Chem. , vol.29 , pp. 1675-1683
    • Huang, L.T.1    Gromiha, M.M.2
  • 40
    • 35648931551 scopus 로고    scopus 로고
    • On the role of structural class of a protein with two-state folding kinetics in determining correlations between its size, topology, and folding rate
    • Istomin A.Y., Jacobs D.J., Livesay D.R. On the role of structural class of a protein with two-state folding kinetics in determining correlations between its size, topology, and folding rate. Protein Sci. 2007, 16:2564-2569.
    • (2007) Protein Sci. , vol.16 , pp. 2564-2569
    • Istomin, A.Y.1    Jacobs, D.J.2    Livesay, D.R.3
  • 41
    • 2942689229 scopus 로고    scopus 로고
    • Prediction of protein folding rates from the amino acid sequence-predicted secondary structure
    • Ivankov D.N., Finkelstein A.V. Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proc. Natl. Acad. Sci. USA 2004, 101:8942-8944.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 8942-8944
    • Ivankov, D.N.1    Finkelstein, A.V.2
  • 43
    • 33847367710 scopus 로고    scopus 로고
    • Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics
    • Huang J.T., Cheng J.P., Chen H. Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics. Proteins: Struct. Funct. Bioinformatics 2007, 67:12-17.
    • (2007) Proteins: Struct. Funct. Bioinformatics , vol.67 , pp. 12-17
    • Huang, J.T.1    Cheng, J.P.2    Chen, H.3
  • 44
    • 64549141572 scopus 로고    scopus 로고
    • Prediction of protein folding rates from primary sequences using hybrid sequence representation
    • Jiang Y.F., Iglinski P., Kurgan L. Prediction of protein folding rates from primary sequences using hybrid sequence representation. J. Comput. Chem. 2009, 30:772-783.
    • (2009) J. Comput. Chem. , vol.30 , pp. 772-783
    • Jiang, Y.F.1    Iglinski, P.2    Kurgan, L.3
  • 45
    • 56949090293 scopus 로고    scopus 로고
    • QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling
    • Li J.Z., Lei B.L., Liu H.X., Li S.Y., Yao X.J., Liu M.C., Gramatica P. QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling. J. Comput. Chem. 2008, 29:2636-2647.
    • (2008) J. Comput. Chem. , vol.29 , pp. 2636-2647
    • Li, J.Z.1    Lei, B.L.2    Liu, H.X.3    Li, S.Y.4    Yao, X.J.5    Liu, M.C.6    Gramatica, P.7
  • 46
    • 33747816816 scopus 로고    scopus 로고
    • PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
    • Li Z.R., Lin H.H., Han L.Y., Jiang L., Chen X., Chen Y.Z. PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res. 2006, 34:W32-W37.
    • (2006) Nucleic Acids Res. , vol.34
    • Li, Z.R.1    Lin, H.H.2    Han, L.Y.3    Jiang, L.4    Chen, X.5    Chen, Y.Z.6
  • 47
    • 0034874330 scopus 로고    scopus 로고
    • Accurate prediction of protein secondary structural content
    • Lin Z., Pan X.M. Accurate prediction of protein secondary structural content. J. Protein Chem. 2001, 20:217-220.
    • (2001) J. Protein Chem. , vol.20 , pp. 217-220
    • Lin, Z.1    Pan, X.M.2
  • 48
    • 33845277149 scopus 로고    scopus 로고
    • QSAR prediction of estrogen activity for a large set of diverse chemicals under the guidance of OECD principles
    • Liu H.X., Papa E., Gramatica P. QSAR prediction of estrogen activity for a large set of diverse chemicals under the guidance of OECD principles. Chem. Res. Toxicol. 2006, 19:1540-1548.
    • (2006) Chem. Res. Toxicol. , vol.19 , pp. 1540-1548
    • Liu, H.X.1    Papa, E.2    Gramatica, P.3
  • 49
    • 33749035288 scopus 로고    scopus 로고
    • Direct correlation between proteins' folding rates and their amino acid compositions: an ab initio folding rate prediction
    • Ma B.G., Guo J.X., Zhang H.Y. Direct correlation between proteins' folding rates and their amino acid compositions: an ab initio folding rate prediction. Proteins 2006, 65:362-372.
    • (2006) Proteins , vol.65 , pp. 362-372
    • Ma, B.G.1    Guo, J.X.2    Zhang, H.Y.3
  • 51
    • 0037133574 scopus 로고    scopus 로고
    • How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
    • Makarov D.E., Keller C.A., Plaxco K.W., Metiu H. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc. Natl. Acad. Sci. USA 2002, 99:3535-3539.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 3535-3539
    • Makarov, D.E.1    Keller, C.A.2    Plaxco, K.W.3    Metiu, H.4
  • 53
    • 0036678120 scopus 로고    scopus 로고
    • Experimental evaluation of topological parameters determining protein-folding rates
    • Miller E.J., Fischer K.F., Marqusee S. Experimental evaluation of topological parameters determining protein-folding rates. Proc. Natl. Acad. Sci. USA 2002, 99:10359-10363.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 10359-10363
    • Miller, E.J.1    Fischer, K.F.2    Marqusee, S.3
  • 54
    • 0001057103 scopus 로고
    • Autocorrelation of a topological structure: a new molecular descriptor
    • Moreau G., Broto P. Autocorrelation of a topological structure: a new molecular descriptor. Nouv. J. Chim. 1980, 4:359-360.
    • (1980) Nouv. J. Chim. , vol.4 , pp. 359-360
    • Moreau, G.1    Broto, P.2
  • 55
    • 0033613165 scopus 로고    scopus 로고
    • A simple model for calculating the kinetics of protein folding from three-dimensional structures
    • Muñoz V., Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. USA 1999, 96:11311-11316.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11311-11316
    • Muñoz, V.1    Eaton, W.A.2
  • 56
    • 12944309313 scopus 로고    scopus 로고
    • Scaling of folding times with protein size
    • Naganathan A.N., Munoz V. Scaling of folding times with protein size. J. Am. Chem. Soc. 2005, 127:480-481.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 480-481
    • Naganathan, A.N.1    Munoz, V.2
  • 57
    • 1042265247 scopus 로고    scopus 로고
    • Approaches to measure chemical similarity-a review
    • Nikolova N., Jaworska J. Approaches to measure chemical similarity-a review. QSAR Comb. Sci. 2003, 22:1006-1026.
    • (2003) QSAR Comb. Sci. , vol.22 , pp. 1006-1026
    • Nikolova, N.1    Jaworska, J.2
  • 59
    • 46449120907 scopus 로고    scopus 로고
    • Predicting protein folding rates from geometric contact and amino acid sequence
    • Ouyang Z., Liang J. Predicting protein folding rates from geometric contact and amino acid sequence. Protein Sci. 2008, 17:1256-1263.
    • (2008) Protein Sci. , vol.17 , pp. 1256-1263
    • Ouyang, Z.1    Liang, J.2
  • 60
    • 33847110311 scopus 로고    scopus 로고
    • Lazy learning-based online identification and adaptive PID control: a case study for CSTR process
    • Pan T., Li S., Cai W.J. Lazy learning-based online identification and adaptive PID control: a case study for CSTR process. Ind. Eng. Chem. Res. 2007, 46:472-480.
    • (2007) Ind. Eng. Chem. Res. , vol.46 , pp. 472-480
    • Pan, T.1    Li, S.2    Cai, W.J.3
  • 61
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 1998, 277:985-994.
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 62
    • 33645240906 scopus 로고    scopus 로고
    • Prediction of folding rates of small proteins: empirical relations based on length, secondary structure content, residue type, and stability
    • Prabhu N.P., Bhuyan A.K. Prediction of folding rates of small proteins: empirical relations based on length, secondary structure content, residue type, and stability. Biochemistry 2006, 45:3805-3812.
    • (2006) Biochemistry , vol.45 , pp. 3805-3812
    • Prabhu, N.P.1    Bhuyan, A.K.2
  • 63
    • 17144369578 scopus 로고    scopus 로고
    • Protein folding rates estimated from contact predictions
    • Punta M., Rost B. Protein folding rates estimated from contact predictions. J. Mol. Biol. 2005, 348:507-512.
    • (2005) J. Mol. Biol. , vol.348 , pp. 507-512
    • Punta, M.1    Rost, B.2
  • 64
    • 21444454088 scopus 로고    scopus 로고
    • PROFcon: novel prediction of long-range contacts
    • Punta M., Rost B. PROFcon: novel prediction of long-range contacts. Bioinformatics 2005, 21:2960-2968.
    • (2005) Bioinformatics , vol.21 , pp. 2960-2968
    • Punta, M.1    Rost, B.2
  • 65
    • 0030814427 scopus 로고    scopus 로고
    • An update of the DEF database of protein fold class predictions
    • Reczko M., Karras D., Bohr H. An update of the DEF database of protein fold class predictions. Nucleic Acids Res. 1997, 25:235.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 235
    • Reczko, M.1    Karras, D.2    Bohr, H.3
  • 66
    • 0028467707 scopus 로고
    • Application of genetic function approximation to quantitative structure-activity relationships and quantitative structure-property relationships
    • Rogers D., Hopfinger A.J. Application of genetic function approximation to quantitative structure-activity relationships and quantitative structure-property relationships. J. Chem. Inf. Comput. Sci. 1994, 34:854-866.
    • (1994) J. Chem. Inf. Comput. Sci. , vol.34 , pp. 854-866
    • Rogers, D.1    Hopfinger, A.J.2
  • 67
    • 0037566828 scopus 로고    scopus 로고
    • A simple parameter relating sequences with folding rates of small alpha helical proteins
    • Shao H., Peng Y., Zeng Z.H. A simple parameter relating sequences with folding rates of small alpha helical proteins. Protein Peptide Lett. 2003, 10:277-280.
    • (2003) Protein Peptide Lett. , vol.10 , pp. 277-280
    • Shao, H.1    Peng, Y.2    Zeng, Z.H.3
  • 68
    • 33747880465 scopus 로고    scopus 로고
    • Ensemble classifier for protein fold pattern recognition
    • Shen H.B., Chou K.C. Ensemble classifier for protein fold pattern recognition. Bioinformatics 2006, 22:1717-1722.
    • (2006) Bioinformatics , vol.22 , pp. 1717-1722
    • Shen, H.B.1    Chou, K.C.2
  • 69
    • 37549004451 scopus 로고    scopus 로고
    • PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition
    • Shen H.B., Chou K.C. PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition. Anal. Biochem. 2008, 373:386-388.
    • (2008) Anal. Biochem. , vol.373 , pp. 386-388
    • Shen, H.B.1    Chou, K.C.2
  • 70
    • 69949110263 scopus 로고    scopus 로고
    • Prediction of protein folding rates from primary sequence by fusing multiple sequential features
    • Shen H.B., Song J.N., Chou K.C. Prediction of protein folding rates from primary sequence by fusing multiple sequential features. J. Biomed. Sci. Eng. 2009, 2:136-143.
    • (2009) J. Biomed. Sci. Eng. , vol.2 , pp. 136-143
    • Shen, H.B.1    Song, J.N.2    Chou, K.C.3
  • 71
    • 29244463544 scopus 로고    scopus 로고
    • Population structure inferred by local spatial autocorrelation: An example from an Amerindian tribal population
    • Sokal R.R., Thomson B.A. Population structure inferred by local spatial autocorrelation: An example from an Amerindian tribal population. Am. J. Phys. Anthropol. 2006, 129:121-131.
    • (2006) Am. J. Phys. Anthropol. , vol.129 , pp. 121-131
    • Sokal, R.R.1    Thomson, B.A.2
  • 72
    • 0029922443 scopus 로고    scopus 로고
    • Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
    • Tomii K., Kanehisa M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 1996, 9:27-36.
    • (1996) Protein Eng. , vol.9 , pp. 27-36
    • Tomii, K.1    Kanehisa, M.2
  • 73
    • 0034663581 scopus 로고    scopus 로고
    • Side-chain conformational entropy in protein unfolded states
    • Trevor P.C. Side-chain conformational entropy in protein unfolded states. Proteins: Struct. Funct. Genet. 2000, 40:443-450.
    • (2000) Proteins: Struct. Funct. Genet. , vol.40 , pp. 443-450
    • Trevor, P.C.1
  • 74
    • 0038724207 scopus 로고    scopus 로고
    • The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models
    • Tropsha A., Gramatica P., Gombar V.K. The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models. QSAR Comb. Sci. 2003, 22:69-77.
    • (2003) QSAR Comb. Sci. , vol.22 , pp. 69-77
    • Tropsha, A.1    Gramatica, P.2    Gombar, V.K.3
  • 75
    • 0027943145 scopus 로고
    • Comparing the predictive accuracy of models using a simple randomization test
    • van der Voet H. Comparing the predictive accuracy of models using a simple randomization test. Chemometrics Intell. Lab. Syst. 1994, 25:313-323.
    • (1994) Chemometrics Intell. Lab. Syst. , vol.25 , pp. 313-323
    • van der Voet, H.1
  • 76
    • 0028851251 scopus 로고    scopus 로고
    • Autocorrelation of molecular surface properties for modeling corticosteroid binding globulin and cytosolic ah receptor activity by neural networks
    • Wagener M., Sadowski J., Gasteiger J. Autocorrelation of molecular surface properties for modeling corticosteroid binding globulin and cytosolic ah receptor activity by neural networks. J. Am. Chem. Soc. 2002, 117:7769-7775.
    • (2002) J. Am. Chem. Soc. , vol.117 , pp. 7769-7775
    • Wagener, M.1    Sadowski, J.2    Gasteiger, J.3
  • 77
    • 0033968062 scopus 로고    scopus 로고
    • Chemoinformatics-similarity and diversity in chemical libraries
    • Willett P. Chemoinformatics-similarity and diversity in chemical libraries. Curr. Opin. Biotechnol. 2000, 11:85-88.
    • (2000) Curr. Opin. Biotechnol. , vol.11 , pp. 85-88
    • Willett, P.1
  • 78
    • 72449157094 scopus 로고    scopus 로고
    • A combined molecular modeling study on gelatinases and their potent inhibitors
    • Xi L.L., Du J., Li S.Y., Li J.Z., Liu H.X., Yao X.J. A combined molecular modeling study on gelatinases and their potent inhibitors. J. Comput. Chem. 2010, 31:24-42.
    • (2010) J. Comput. Chem. , vol.31 , pp. 24-42
    • Xi, L.L.1    Du, J.2    Li, S.Y.3    Li, J.Z.4    Liu, H.X.5    Yao, X.J.6
  • 79
    • 13244258262 scopus 로고    scopus 로고
    • Mapping protein energy landscapes with amide hydrogen exchange and mass spectrometry: I. A generalized model for a two-state protein and comparison with experiment
    • Xiao H., Hoerner J.K., Eyles S.J., Dobo A., Voigtman E., Mel'cuk A.I., Kaltashov I.A. Mapping protein energy landscapes with amide hydrogen exchange and mass spectrometry: I. A generalized model for a two-state protein and comparison with experiment. Protein Sci. 2005, 14:543-557.
    • (2005) Protein Sci. , vol.14 , pp. 543-557
    • Xiao, H.1    Hoerner, J.K.2    Eyles, S.J.3    Dobo, A.4    Voigtman, E.5    Mel'cuk, A.I.6    Kaltashov, I.A.7
  • 80
    • 3342898158 scopus 로고    scopus 로고
    • Protein folding studied by real-time NMR spectroscopy
    • Zeeb M., Balbach J. Protein folding studied by real-time NMR spectroscopy. Methods 2004, 34:65-74.
    • (2004) Methods , vol.34 , pp. 65-74
    • Zeeb, M.1    Balbach, J.2
  • 81
    • 33750321978 scopus 로고    scopus 로고
    • A novel automated lazy learning QSAR (ALL-QSAR) approach: method development, applications, and virtual screening of chemical databases using validated ALL-QSAR models
    • Zhang S., Golbraikh A., Oloff S., Kohn H., Tropsha A. A novel automated lazy learning QSAR (ALL-QSAR) approach: method development, applications, and virtual screening of chemical databases using validated ALL-QSAR models. J. Chem. Inf. Model. 2006, 46:1984-1995.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1984-1995
    • Zhang, S.1    Golbraikh, A.2    Oloff, S.3    Kohn, H.4    Tropsha, A.5
  • 82
    • 0036215854 scopus 로고    scopus 로고
    • Folding rate prediction using total contact distance
    • Zhou H.Y., Zhou Y.Q. Folding rate prediction using total contact distance. Biophys. J. 2002, 82:458-463.
    • (2002) Biophys. J. , vol.82 , pp. 458-463
    • Zhou, H.Y.1    Zhou, Y.Q.2


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