메뉴 건너뛰기




Volumn 6, Issue SUPPL.1, 2012, Pages

A novel neural response algorithm for protein function prediction

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84875807798     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-S1-S19     Document Type: Article
Times cited : (5)

References (44)
  • 1
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • 10.1093/nar/gkh063, 308797, 14681412
    • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-280. 10.1093/nar/gkh063, 308797, 14681412.
    • (2004) Nucleic Acids Res , vol.32
    • Kanehisa, M.1    Goto, S.2    Kawashima, S.3    Okuno, Y.4    Hattori, M.5
  • 2
    • 34248155322 scopus 로고    scopus 로고
    • Function prediction of uncharacterized proteins
    • 10.1142/S0219720007002503, 17477489
    • Hawkins T, Kihara D. Function prediction of uncharacterized proteins. J Bioinform Comput Biol 2007, 5(1):1-30. 10.1142/S0219720007002503, 17477489.
    • (2007) J Bioinform Comput Biol , vol.5 , Issue.1 , pp. 1-30
    • Hawkins, T.1    Kihara, D.2
  • 3
    • 59849089151 scopus 로고    scopus 로고
    • PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
    • 10.1002/prot.22172, 18655063
    • Hawkins T, Chitale M, Luban S, Kihara D. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins 2009, 74(3):566-582. 10.1002/prot.22172, 18655063.
    • (2009) Proteins , vol.74 , Issue.3 , pp. 566-582
    • Hawkins, T.1    Chitale, M.2    Luban, S.3    Kihara, D.4
  • 4
    • 0346799108 scopus 로고    scopus 로고
    • Prediction of protein function from protein sequence and structure
    • 10.1017/S0033583503003901, 15029827
    • Whisstock JC, Lesk AM. Prediction of protein function from protein sequence and structure. Q Rev Biophys 2003, 36(3):307-340. 10.1017/S0033583503003901, 15029827.
    • (2003) Q Rev Biophys , vol.36 , Issue.3 , pp. 307-340
    • Whisstock, J.C.1    Lesk, A.M.2
  • 5
    • 0033964710 scopus 로고    scopus 로고
    • From genes to protein structure and function: novel applications of computational approaches in the genomic era
    • 10.1016/S0167-7799(99)01398-0, 10631780
    • Skolnick J, Fetrow JS. From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends Biotechnol 2000, 18(1):34-39. 10.1016/S0167-7799(99)01398-0, 10631780.
    • (2000) Trends Biotechnol , vol.18 , Issue.1 , pp. 34-39
    • Skolnick, J.1    Fetrow, J.S.2
  • 6
    • 0346731042 scopus 로고    scopus 로고
    • Automatic prediction of protein function
    • 10.1007/s00018-003-3114-8, 14685688
    • Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y. Automatic prediction of protein function. Cell Mol Life Sci 2003, 60(12):2637-2650. 10.1007/s00018-003-3114-8, 14685688.
    • (2003) Cell Mol Life Sci , vol.60 , Issue.12 , pp. 2637-2650
    • Rost, B.1    Liu, J.2    Nair, R.3    Wrzeszczynski, K.O.4    Ofran, Y.5
  • 7
    • 0029006062 scopus 로고
    • The multiplicity of domains in proteins
    • 10.1146/annurev.bi.64.070195.001443, 7574483
    • Doolittle RF. The multiplicity of domains in proteins. Annu Rev Biochem 1995, 64:287-314. 10.1146/annurev.bi.64.070195.001443, 7574483.
    • (1995) Annu Rev Biochem , vol.64 , pp. 287-314
    • Doolittle, R.F.1
  • 8
    • 20444456581 scopus 로고    scopus 로고
    • Automatic annotation of protein function
    • 10.1016/j.sbi.2005.05.010, 15922590
    • Valencia A. Automatic annotation of protein function. Curr Opin Struct Biol 2005, 15(3):267-274. 10.1016/j.sbi.2005.05.010, 15922590.
    • (2005) Curr Opin Struct Biol , vol.15 , Issue.3 , pp. 267-274
    • Valencia, A.1
  • 9
    • 0033194958 scopus 로고    scopus 로고
    • Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB), Enzyme Supplement 5 (1999)
    • Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB), Enzyme Supplement 5 (1999). Eur J Biochem 1999, 264(2):610-650.
    • (1999) Eur J Biochem , vol.264 , Issue.2 , pp. 610-650
  • 12
    • 0034674164 scopus 로고    scopus 로고
    • Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits
    • 10.1006/jmbi.2000.3763, 10843865
    • Gille C, Goede A, Preissner R, Rother K, Frommel C. Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits. J Mol Biol 2000, 299(4):1147-1154. 10.1006/jmbi.2000.3763, 10843865.
    • (2000) J Mol Biol , vol.299 , Issue.4 , pp. 1147-1154
    • Gille, C.1    Goede, A.2    Preissner, R.3    Rother, K.4    Frommel, C.5
  • 13
    • 0034677669 scopus 로고    scopus 로고
    • Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
    • 10.1006/jmbi.2000.3550, 10704319
    • Wilson CA, Kreychman J, Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 2000, 297(1):233-249. 10.1006/jmbi.2000.3550, 10704319.
    • (2000) J Mol Biol , vol.297 , Issue.1 , pp. 233-249
    • Wilson, C.A.1    Kreychman, J.2    Gerstein, M.3
  • 14
    • 11844292002 scopus 로고    scopus 로고
    • Inference of protein function from protein structure
    • 10.1016/j.str.2004.10.015, 15642267
    • Pal D, Eisenberg D. Inference of protein function from protein structure. Structure 2005, 13(1):121-130. 10.1016/j.str.2004.10.015, 15642267.
    • (2005) Structure , vol.13 , Issue.1 , pp. 121-130
    • Pal, D.1    Eisenberg, D.2
  • 15
    • 13944252921 scopus 로고    scopus 로고
    • Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology
    • 10.1002/prot.20355, 15645518
    • Ponomarenko JV, Bourne PE, Shindyalov IN. Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins 2005, 58(4):855-865. 10.1002/prot.20355, 15645518.
    • (2005) Proteins , vol.58 , Issue.4 , pp. 855-865
    • Ponomarenko, J.V.1    Bourne, P.E.2    Shindyalov, I.N.3
  • 16
    • 0030777303 scopus 로고    scopus 로고
    • CATH--a hierarchic classification of protein domain structures
    • 10.1016/S0969-2126(97)00260-8, 9309224
    • Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH--a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093-1108. 10.1016/S0969-2126(97)00260-8, 9309224.
    • (1997) Structure , vol.5 , Issue.8 , pp. 1093-1108
    • Orengo, C.A.1    Michie, A.D.2    Jones, S.3    Jones, D.T.4    Swindells, M.B.5    Thornton, J.M.6
  • 17
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.
    • (1995) J Mol Biol , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 19
    • 0032926060 scopus 로고    scopus 로고
    • The CATH Database provides insights into protein structure/function relationships
    • 10.1093/nar/27.1.275, 148155, 9847200
    • Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM. The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res 1999, 27(1):275-279. 10.1093/nar/27.1.275, 148155, 9847200.
    • (1999) Nucleic Acids Res , vol.27 , Issue.1 , pp. 275-279
    • Orengo, C.A.1    Pearl, F.M.2    Bray, J.E.3    Todd, A.E.4    Martin, A.C.5    Lo Conte, L.6    Thornton, J.M.7
  • 21
    • 3242892059 scopus 로고    scopus 로고
    • GOblet: a platform for Gene Ontology annotation of anonymous sequence data
    • 10.1093/nar/gkh406, 441544, 15215401
    • Groth D, Lehrach H, Hennig S. GOblet: a platform for Gene Ontology annotation of anonymous sequence data. Nucleic Acids Res 2004, 32:W313-317. 10.1093/nar/gkh406, 441544, 15215401.
    • (2004) Nucleic Acids Res , vol.32
    • Groth, D.1    Lehrach, H.2    Hennig, S.3
  • 22
    • 0043122923 scopus 로고    scopus 로고
    • OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms
    • 10.1093/nar/gkg555, 168962, 12824422
    • Zehetner G. OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. Nucleic Acids Res 2003, 31(13):3799-3803. 10.1093/nar/gkg555, 168962, 12824422.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3799-3803
    • Zehetner, G.1
  • 23
    • 0348143187 scopus 로고    scopus 로고
    • GoFigure: automated Gene Ontology annotation
    • 10.1093/bioinformatics/btg338, 14668239
    • Khan S, Situ G, Decker K, Schmidt CJ. GoFigure: automated Gene Ontology annotation. Bioinformatics 2003, 19(18):2484-2485. 10.1093/bioinformatics/btg338, 14668239.
    • (2003) Bioinformatics , vol.19 , Issue.18 , pp. 2484-2485
    • Khan, S.1    Situ, G.2    Decker, K.3    Schmidt, C.J.4
  • 24
    • 13244268370 scopus 로고    scopus 로고
    • GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
    • 10.1186/1471-2105-5-178, 535938, 15550167
    • Martin DM, Berriman M, Barton GJ. GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 2004, 5:178. 10.1186/1471-2105-5-178, 535938, 15550167.
    • (2004) BMC Bioinformatics , vol.5 , pp. 178
    • Martin, D.M.1    Berriman, M.2    Barton, G.J.3
  • 25
    • 33744471931 scopus 로고    scopus 로고
    • Enhanced automated function prediction using distantly related sequences and contextual association by PFP
    • 10.1110/ps.062153506, 2242549, 16672240
    • Hawkins T, Luban S, Kihara D. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Science 2006, 15(6):1550-1556. 10.1110/ps.062153506, 2242549, 16672240.
    • (2006) Protein Science , vol.15 , Issue.6 , pp. 1550-1556
    • Hawkins, T.1    Luban, S.2    Kihara, D.3
  • 26
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 27
    • 48449088976 scopus 로고    scopus 로고
    • FFPred: an integrated feature-based function prediction server for vertebrate proteomes
    • 10.1093/nar/gkn193, 2447771, 18463141
    • Lobley AE, Nugent T, Orengo CA, Jones DT. FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res 2008, 36:W297-302. 10.1093/nar/gkn193, 2447771, 18463141.
    • (2008) Nucleic Acids Res , vol.36
    • Lobley, A.E.1    Nugent, T.2    Orengo, C.A.3    Jones, D.T.4
  • 29
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: a web server for clustering and comparing biological sequences
    • 10.1093/bioinformatics/btq003, 2828112, 20053844
    • Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010, 26(5):680-682. 10.1093/bioinformatics/btq003, 2828112, 20053844.
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 680-682
    • Huang, Y.1    Niu, B.2    Gao, Y.3    Fu, L.4    Li, W.5
  • 30
    • 0025882349 scopus 로고
    • PROSITE: a dictionary of sites and patterns in proteins
    • 10.1093/nar/19.suppl.2241, 331358, 2041810
    • Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res 1991, 19(Suppl):2241-2245. 10.1093/nar/19.suppl.2241, 331358, 2041810.
    • (1991) Nucleic Acids Res , vol.19 , Issue.SUPPL. , pp. 2241-2245
    • Bairoch, A.1
  • 31
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: a comprehensive database of protein domain families based on seed alignments
    • 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L, 9223186
    • Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997, 28(3):405-420. 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L, 9223186.
    • (1997) Proteins , vol.28 , Issue.3 , pp. 405-420
    • Sonnhammer, E.L.1    Eddy, S.R.2    Durbin, R.3
  • 32
    • 0003516147 scopus 로고    scopus 로고
    • Biological sequence analysis: probabilistic models of proteins and nucleic acids
    • Cambridge University Press
    • Durbin R, Eddy S, Krogh A, Mitchison G. Biological sequence analysis: probabilistic models of proteins and nucleic acids. 1998, Cambridge University Press.
    • (1998)
    • Durbin, R.1    Eddy, S.2    Krogh, A.3    Mitchison, G.4
  • 33
    • 0141634362 scopus 로고    scopus 로고
    • Profile-profile comparisons by COMPASS predict intricate homologies between protein families
    • 2366929, 14500884
    • Sadreyev RI, Baker D, Grishin NV. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci 2003, 12(10):2262-2272. 2366929, 14500884.
    • (2003) Protein Sci , vol.12 , Issue.10 , pp. 2262-2272
    • Sadreyev, R.I.1    Baker, D.2    Grishin, N.V.3
  • 34
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • 10.1093/bioinformatics/bti125, 15531603
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21(7):951-960. 10.1093/bioinformatics/bti125, 15531603.
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 951-960
    • Soding, J.1
  • 35
    • 33744779891 scopus 로고    scopus 로고
    • Sequence comparison and protein structure prediction
    • 10.1016/j.sbi.2006.05.006, 16713709
    • Dunbrack RL. Sequence comparison and protein structure prediction. Curr Opin Struct Biol 2006, 16(3):374-384. 10.1016/j.sbi.2006.05.006, 16713709.
    • (2006) Curr Opin Struct Biol , vol.16 , Issue.3 , pp. 374-384
    • Dunbrack, R.L.1
  • 36
    • 0344305738 scopus 로고    scopus 로고
    • Exploring the sequence patterns in the alpha-helices of proteins
    • 10.1093/protein/gzg101, 14631069
    • Wang JW, Feng JA. Exploring the sequence patterns in the alpha-helices of proteins. Protein Engineering 2003, 16(11):799-807. 10.1093/protein/gzg101, 14631069.
    • (2003) Protein Engineering , vol.16 , Issue.11 , pp. 799-807
    • Wang, J.W.1    Feng, J.A.2
  • 37
    • 12944288129 scopus 로고    scopus 로고
    • NdPASA: A novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities
    • Wang JW, Feng JA. NdPASA: A novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities. Proteins 2005, 58(3):628-637.
    • (2005) Proteins , vol.58 , Issue.3 , pp. 628-637
    • Wang, J.W.1    Feng, J.A.2
  • 38
    • 27544439431 scopus 로고    scopus 로고
    • NdPASA: a pairwise sequence alignment server for distantly related proteins
    • 10.1093/bioinformatics/bti619, 16105904
    • Li W, Wang JW, Feng JA. NdPASA: a pairwise sequence alignment server for distantly related proteins. Bioinformatics 2005, 21(19):3803-3805. 10.1093/bioinformatics/bti619, 16105904.
    • (2005) Bioinformatics , vol.21 , Issue.19 , pp. 3803-3805
    • Li, W.1    Wang, J.W.2    Feng, J.A.3
  • 39
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • 10.1093/bioinformatics/16.4.404, 10869041
    • McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000, 16(4):404-405. 10.1093/bioinformatics/16.4.404, 10869041.
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 40
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • 10.1093/nar/gki408, 1160169, 15980461
    • Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005, 33:W244-248. 10.1093/nar/gki408, 1160169, 15980461.
    • (2005) Nucleic Acids Res , vol.33
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 41
    • 0001244666 scopus 로고    scopus 로고
    • ScanProsite: a reference implementation of a PROSITE scanning tool
    • Gattiker A, Gasteiger E, Bairoch A. ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics 2002, 1(2):107-108.
    • (2002) Appl Bioinformatics , vol.1 , Issue.2 , pp. 107-108
    • Gattiker, A.1    Gasteiger, E.2    Bairoch, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.