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Volumn 12, Issue 3-4, 2008, Pages 171-179

Prediction of protein structural classes using hybrid properties

Author keywords

Amino acid compositions; MRMR (Minimum Redundancy, Maximum Relevance); Nearest neighbor algorithm; Physiochemical properties; Protein structural class

Indexed keywords

HYBRID PROTEIN; AMINO ACID; PROTEIN;

EID: 60549098659     PISSN: 13811991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11030-008-9093-9     Document Type: Article
Times cited : (16)

References (35)
  • 1
    • 0029157083 scopus 로고
    • Prediction of protein structural classes
    • 10.3109/10409239509083488
    • KC Chou CT Zhang 1995 Prediction of protein structural classes Crit Rev Biochem Mol Biol 30 275 349 10.3109/10409239509083488
    • (1995) Crit Rev Biochem Mol Biol , vol.30 , pp. 275-349
    • Chou, K.C.1    Zhang, C.T.2
  • 2
    • 0018110116 scopus 로고
    • Prediction of the secondary structure of proteins from their amino acid sequence
    • PY Chou GD Fasman 1978 Prediction of the secondary structure of proteins from their amino acid sequence Adv Enzymol Relat Areas Mol Biol 47 45 148
    • (1978) Adv Enzymol Relat Areas Mol Biol , vol.47 , pp. 45-148
    • Chou, P.Y.1    Fasman, G.D.2
  • 3
    • 0022777472 scopus 로고
    • Prediction of protein structural class from the amino acid sequence
    • 10.1002/bip.360250909
    • P Klein C Delisi 1986 Prediction of protein structural class from the amino acid sequence Biopolymers 25 1659 1672 10.1002/bip.360250909
    • (1986) Biopolymers , vol.25 , pp. 1659-1672
    • Klein, P.1    Delisi, C.2
  • 4
    • 0022631926 scopus 로고
    • The folding type of a protein is relevant to the amino acid composition
    • H Nakashima K Nishikawa T Ooi 1986 The folding type of a protein is relevant to the amino acid composition J Biochem 99 153 162
    • (1986) J Biochem , vol.99 , pp. 153-162
    • Nakashima, H.1    Nishikawa, K.2    Ooi, T.3
  • 5
    • 0027080161 scopus 로고
    • An optimization approach to predicting protein structural class from amino acid composition
    • CT Zhang KC Chou 1992 An optimization approach to predicting protein structural class from amino acid composition Protein Sci 1 401 408
    • (1992) Protein Sci , vol.1 , pp. 401-408
    • Zhang, C.T.1    Chou, K.C.2
  • 6
    • 0031928664 scopus 로고    scopus 로고
    • Domain structural class prediction
    • 10.1093/protein/11.7.523
    • KC Chou GM Maggiora 1998 Domain structural class prediction Protein Eng 11 523 538 10.1093/protein/11.7.523
    • (1998) Protein Eng , vol.11 , pp. 523-538
    • Chou, K.C.1    Maggiora, G.M.2
  • 7
    • 0026636320 scopus 로고
    • A correlation-coefficient method to predicting protein-structural classes from amino acid compositions
    • 10.1111/j.1432-1033.1992.tb17067.x
    • KC Chou CT Zhang 1992 A correlation-coefficient method to predicting protein-structural classes from amino acid compositions Eur J Biochem 207 429 433 10.1111/j.1432-1033.1992.tb17067.x
    • (1992) Eur J Biochem , vol.207 , pp. 429-433
    • Chou, K.C.1    Zhang, C.T.2
  • 8
    • 28444439947 scopus 로고    scopus 로고
    • Using LogitBoost classifier to predict protein structural classes
    • 10.1016/j.jtbi.2005.05.034
    • YD Cai KY Feng WC Lu KC Chou 2006 Using LogitBoost classifier to predict protein structural classes J Theor Biol 238 172 176 10.1016/j.jtbi.2005.05.034
    • (2006) J Theor Biol , vol.238 , pp. 172-176
    • Cai, Y.D.1    Feng, K.Y.2    Lu, W.C.3    Chou, K.C.4
  • 9
    • 33644889341 scopus 로고    scopus 로고
    • Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor
    • 10.1002/jcc.20354
    • X Xiao SH Shao ZD Huang KC Chou 2006 Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor J Comput Chem 27 478 482 10.1002/jcc.20354
    • (2006) J Comput Chem , vol.27 , pp. 478-482
    • Xiao, X.1    Shao, S.H.2    Huang, Z.D.3    Chou, K.C.4
  • 10
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • 10.1073/pnas.92.19.8700
    • I Dubchak I Muchnik SR Holbrook SH Kim 1995 Prediction of protein folding class using global description of amino acid sequence Proc Natl Acad Sci USA 92 8700 8704 10.1073/pnas.92.19.8700
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchnik, I.2    Holbrook, S.R.3    Kim, S.H.4
  • 11
    • 0034141493 scopus 로고    scopus 로고
    • How good is prediction of protein structural class by the component-coupled method?
    • doi:10.1002/(SICI)1097-0134(20000201)38:2<165::AID-PROT5>3.0.CO;2-V
    • Wang ZX, Yuan Z (2000) How good is prediction of protein structural class by the component-coupled method? Proteins 38:165-175. doi:10.1002/(SICI)1097- 0134(20000201)38:2<165::AID-PROT5>3.0.CO;2-V
    • (2000) Proteins , vol.38 , pp. 165-175
    • Wang, Z.X.1    Yuan, Z.2
  • 12
    • 3843117638 scopus 로고    scopus 로고
    • Predicting protein structural class by functional domain composition
    • 10.1016/j.bbrc.2004.07.059
    • KC Chou YD Cai 2004 Predicting protein structural class by functional domain composition Biochem Biophys Res Commun 321 1007 1009 10.1016/j.bbrc.2004. 07.059
    • (2004) Biochem Biophys Res Commun , vol.321 , pp. 1007-1009
    • Chou, K.C.1    Cai, Y.D.2
  • 13
    • 32644441676 scopus 로고    scopus 로고
    • Prediction of protein structural class with Rough Sets
    • 10.1186/1471-2105-7-20
    • Y Cao S Liu L Zhang J Qin J Wang K Tang 2006 Prediction of protein structural class with Rough Sets BMC Bioinformatics 7 1 6 10.1186/1471-2105-7-20
    • (2006) BMC Bioinformatics , vol.7 , pp. 1-6
    • Cao, Y.1    Liu, S.2    Zhang, L.3    Qin, J.4    Wang, J.5    Tang, K.6
  • 14
    • 34548697717 scopus 로고    scopus 로고
    • Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network
    • 10.2174/092986607781483778
    • YS Ding TL Zhang KC Chou 2007 Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network Protein Pept Lett 14 811 815 10.2174/092986607781483778
    • (2007) Protein Pept Lett , vol.14 , pp. 811-815
    • Ding, Y.S.1    Zhang, T.L.2    Chou, K.C.3
  • 15
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: Criteria of max-dependency, max-relevance, and min-redundancy
    • 10.1109/TPAMI.2005.159
    • H Peng F Long C Ding 2005 Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy IEEE Trans Pattern Anal Mach Intell 27 1226 1238 10.1109/TPAMI.2005.159
    • (2005) IEEE Trans Pattern Anal Mach Intell , vol.27 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 16
    • 0038705861 scopus 로고    scopus 로고
    • Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition
    • 10.1016/S0006-291X(03)00775-7
    • YD Cai KC Chou 2003 Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition Biochem Biophys Res Commun 305 407 411 10.1016/S0006-291X(03) 00775-7
    • (2003) Biochem Biophys Res Commun , vol.305 , pp. 407-411
    • Cai, Y.D.1    Chou, K.C.2
  • 17
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • AG Murzin SE Brenner T Hubbard C Chothia 1995 SCOP: a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536 540
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 22
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • 10.1093/nar/28.1.254
    • SE Brenner P Koehl M Levitt 2000 The ASTRAL compendium for protein structure and sequence analysis Nucleic Acids Res 28 254 256 10.1093/nar/28.1.254
    • (2000) Nucleic Acids Res , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 23
    • 0033151954 scopus 로고    scopus 로고
    • Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification
    • doi:10.1002/(SICI)1097-0134(19990601)35:4<401::AID-PROT3>3.0.CO;2-K
    • Dubchak I, Muchnik I, Mayor C, Dralyuk I, Kim SH (1999) Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification. Proteins 35:401-407. doi:10.1002/(SICI)1097-0134(19990601)35: 4<401::AID-PROT3>3.0.CO;2-K
    • (1999) Proteins , vol.35 , pp. 401-407
    • Dubchak, I.1    Muchnik, I.2    Mayor, C.3    Dralyuk, I.4    Kim, S.H.5
  • 24
    • 0033049071 scopus 로고    scopus 로고
    • PredAcc: Prediction of solvent accessibility
    • 10.1093/bioinformatics/15.2.176
    • MH Mucchielli-Giorgi S Hazout P Tuffery 1999 PredAcc: prediction of solvent accessibility Bioinformatics 15 176 177 10.1093/bioinformatics/15.2.176
    • (1999) Bioinformatics , vol.15 , pp. 176-177
    • Mucchielli-Giorgi, M.H.1    Hazout, S.2    Tuffery, P.3
  • 25
    • 17644384367 scopus 로고    scopus 로고
    • Minimum redundancy feature selection from microarray gene expression data
    • 10.1142/S0219720005001004
    • C Ding H Peng 2005 Minimum redundancy feature selection from microarray gene expression data J Bioinform Comput Biol 3 185 205 10.1142/S0219720005001004
    • (2005) J Bioinform Comput Biol , vol.3 , pp. 185-205
    • Ding, C.1    Peng, H.2
  • 26
    • 0029157039 scopus 로고
    • Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions
    • Z Weng RJ Rickles S Feng S Richard AS Shaw SL Schreiber 1995 Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions Mol Cell Biol 15 5627 5634
    • (1995) Mol Cell Biol , vol.15 , pp. 5627-5634
    • Weng, Z.1    Rickles, R.J.2    Feng, S.3    Richard, S.4    Shaw, A.S.5    Schreiber, S.L.6
  • 27
    • 33644865137 scopus 로고    scopus 로고
    • Intrinsic protein disorder, amino acid composition, and histone terminal domains
    • 10.1074/jbc.R500022200
    • JC Hansen X Lu ED Ross RW Woody 2006 Intrinsic protein disorder, amino acid composition, and histone terminal domains J Biol Chem 281 1853 1856 10.1074/jbc.R500022200
    • (2006) J Biol Chem , vol.281 , pp. 1853-1856
    • Hansen, J.C.1    Lu, X.2    Ross, E.D.3    Woody, R.W.4
  • 28
    • 1542400269 scopus 로고    scopus 로고
    • Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
    • 10.1093/bioinformatics/btg432
    • S Ahmad MM Gromiha A Sarai 2004 Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information Bioinformatics 20 477 486 10.1093/bioinformatics/btg432
    • (2004) Bioinformatics , vol.20 , pp. 477-486
    • Ahmad, S.1    Gromiha, M.M.2    Sarai, A.3
  • 29
    • 0032550148 scopus 로고    scopus 로고
    • Solvent accessibility analysis on the mutants of Hsc70 ATPase fragment
    • 10.1016/S0301-4622(97)00137-3
    • TS Kumarevel MM Gromiha MN Ponnuswamy 1998 Solvent accessibility analysis on the mutants of Hsc70 ATPase fragment Biophys Chem 71 99 111 10.1016/S0301-4622(97)00137-3
    • (1998) Biophys Chem , vol.71 , pp. 99-111
    • Kumarevel, T.S.1    Gromiha, M.M.2    Ponnuswamy, M.N.3
  • 30
    • 33646030668 scopus 로고    scopus 로고
    • Role of solvent accessibility in structure based drug design
    • 10.2174/1573409054367664
    • MM Gromiha S Ahmad 2005 Role of solvent accessibility in structure based drug design Curr Comput-Aided Drug Des 1 223 235 10.2174/1573409054367664
    • (2005) Curr Comput-Aided Drug des , vol.1 , pp. 223-235
    • Gromiha, M.M.1    Ahmad, S.2
  • 31
    • 34447506573 scopus 로고    scopus 로고
    • Fold recognition by concurrent use of solvent accessibility and residue depth
    • 10.1002/prot.21459
    • S Liu C Zhang S Liang Y Zhou 2007 Fold recognition by concurrent use of solvent accessibility and residue depth Proteins 68 636 645 10.1002/prot.21459
    • (2007) Proteins , vol.68 , pp. 636-645
    • Liu, S.1    Zhang, C.2    Liang, S.3    Zhou, Y.4
  • 32
    • 33746004284 scopus 로고    scopus 로고
    • Conformational analysis, solvent-accessible surface and geometric extent of inhibitors and substrates
    • 10.1135/cccc20060842
    • M Froeyen H DeWinter P Herdewijn 2006 Conformational analysis, solvent-accessible surface and geometric extent of inhibitors and substrates Collect Czech Chem Commun 71 842 858 10.1135/cccc20060842
    • (2006) Collect Czech Chem Commun , vol.71 , pp. 842-858
    • Froeyen, M.1    Dewinter, H.2    Herdewijn, P.3
  • 33
    • 0025281494 scopus 로고
    • Molecular interactions in protein crystals: Solvent accessible surface and stability
    • 10.1002/prot.340080103
    • SA Islam DL Weaver 1990 Molecular interactions in protein crystals: solvent accessible surface and stability Proteins 8 1 5 10.1002/prot.340080103
    • (1990) Proteins , vol.8 , pp. 1-5
    • Islam, S.A.1    Weaver, D.L.2
  • 34
    • 1842788912 scopus 로고    scopus 로고
    • Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins
    • 10.1002/jcc.10420
    • E Eyal R Najmanovich BJ McConkey M Edelman V Sobolev 2004 Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins J Comput Chem 25 712 724 10.1002/jcc.10420
    • (2004) J Comput Chem , vol.25 , pp. 712-724
    • Eyal, E.1    Najmanovich, R.2    McConkey, B.J.3    Edelman, M.4    Sobolev, V.5
  • 35
    • 62849098047 scopus 로고    scopus 로고
    • Molecular surfaces: A review
    • Connolly ML (1996) Molecular surfaces: A review. Solvent Accessible Surfaces http://www.netsci.org/Science/Compchem/feature14e.html
    • (1996) Solvent Accessible Surfaces
    • Connolly, M.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.