메뉴 건너뛰기




Volumn 19, Issue 15, 2003, Pages 1985-1996

A computational pipeline for protein structure prediction and analysis at genome scale

Author keywords

[No Author keywords available]

Indexed keywords

SIGNAL PEPTIDE;

EID: 0142210248     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg262     Document Type: Article
Times cited : (17)

References (38)
  • 1
    • 0030310296 scopus 로고    scopus 로고
    • Fast protein fold recognition via sequence to structure alignment and contact capacity potentials
    • Alexandrov,N.N., Nussinov,R. and Zimmer,R.M. (1996) Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. Pac Symp Biocomput, 53-72.
    • (1996) Pac. Symp. Biocomput. , pp. 53-72
    • Alexandrov, N.N.1    Nussinov, R.2    Zimmer, R.M.3
  • 4
    • 0027216384 scopus 로고
    • The ENZYME data bank
    • Bairoch,A. (1993) The ENZYME data bank. Nucleic Acids Res., 21, 3155-3156.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 3155-3156
    • Bairoch, A.1
  • 6
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie,J.U., Luthy,R. and Eisenberg,D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 8
    • 0028783819 scopus 로고
    • Protein structure prediction issue
    • CASP
    • CASP (1995) Protein structure prediction issue. Proteins: Struct. Funct. Genet., 23, 295-462.
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 295-462
  • 9
    • 0003183710 scopus 로고    scopus 로고
    • Protein structure prediction issue
    • CASP
    • CASP (1997) Protein structure prediction issue. Proteins: Struct. Funct. Genet., 29 (Suppl. 1), 1-230.
    • (1997) Proteins: Struct. Funct. Genet. , vol.29 , Issue.SUPPL. 1 , pp. 1-230
  • 10
    • 0003183712 scopus 로고    scopus 로고
    • Protein structure prediction issue
    • CASP
    • CASP (1999) Protein structure prediction issue. Proteins: Struct. Funct. Genet., 37 (Suppl. 3), 1-237.
    • (1999) Proteins: Struct. Funct. Genet. , vol.37 , Issue.SUPPL. 3 , pp. 1-237
  • 11
    • 0010299663 scopus 로고    scopus 로고
    • Protein structure prediction issue
    • CASP
    • CASP (2001) Protein structure prediction issue. Proteins: Struct. Funct. Genet., (Suppl. 4), 1-199.
    • (2001) Proteins: Struct. Funct. Genet. , Issue.SUPPL. 4 , pp. 1-199
  • 13
    • 0002053443 scopus 로고
    • Phytoplankton size
    • Falkowski,P.G. and Woodhead,A.D. (eds), Plenum Press, New York
    • Chisholm,S.W. (1992) Phytoplankton size. In Falkowski,P.G. and Woodhead,A.D. (eds), Primary Productivity and Biogeochemical Cycles. Plenum Press, New York, pp. 213-237.
    • (1992) Primary Productivity and Biogeochemical Cycles , pp. 213-237
    • Chisholm, S.W.1
  • 14
    • 0033957841 scopus 로고    scopus 로고
    • ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
    • Corpet,F., Servant,F., Gouzy,J. and Kahn,D. (2000) ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res., 28, 267-269.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 267-269
    • Corpet, F.1    Servant, F.2    Gouzy, J.3    Kahn, D.4
  • 15
    • 0031826040 scopus 로고    scopus 로고
    • Classification and secondary structure prediction system for membrane proteins
    • Hirokawa,T., Boon-Cheing,S. and Mitaku,S. (1998) Classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14, 378-379.
    • (1998) Bioinformatics , vol.14 , pp. 378-379
    • Hirokawa, T.1    Boon-Cheing, S.2    Mitaku, S.3
  • 16
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones,D.T., Taylor,W.R. and Thornton,J.M. (1992) A new approach to protein fold recognition. Nature, 358, 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 17
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 19
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh,A., Larsson,B., von Heijne,G. and Sonnhammer,E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 20
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander,E.C. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.C.1
  • 21
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas,A., Van Dyke,M. and Stock,J. (1991) Predicting coiled coils from protein sequences, Science, 252, 1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 22
    • 0032921818 scopus 로고    scopus 로고
    • Structural genomics: Key-note for a Human Proteome Project
    • Montelione,G.T. and Anderson,S. (1999) Structural genomics: key-note for a Human Proteome Project. Nature Struct. Biol., 6, 11-12.
    • (1999) Nature Struct. Biol. , vol.6 , pp. 11-12
    • Montelione, G.T.1    Anderson, S.2
  • 23
    • 0028961335 scopus 로고
    • Scop: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (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
  • 24
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen,H., Engelbrecht,J., Brunak,S. and von Heijne,G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10, 1-6.
    • (1997) Protein Eng. , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    von Heijne, G.4
  • 25
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 26
    • 0032506030 scopus 로고    scopus 로고
    • Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
    • Sanchez,R. and Sali,A. (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl Acad. Sci. USA., 95, 13597-13602.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 13597-13602
    • Sanchez, R.1    Sali, A.2
  • 27
    • 0142205787 scopus 로고    scopus 로고
    • IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    • Schaffer,A.A., Wolf,Y.I., Ponting,C.P., Koonin,E.V., Aravind,L. and Altschul,S.F. (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 16, 488-489.
    • (1999) Bioinformatics , vol.16 , pp. 488-489
    • Schaffer, A.A.1    Wolf, Y.I.2    Ponting, C.P.3    Koonin, E.V.4    Aravind, L.5    Altschul, S.F.6
  • 28
    • 0026704815 scopus 로고
    • Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations
    • Sippl,M.J. and Weitckus,S. (1992) Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations. Proteins: Struct. Funct. Genet., 13, 258-271.
    • (1992) Proteins: Struct. Funct. Genet. , vol.13 , pp. 258-271
    • Sippl, M.J.1    Weitckus, S.2
  • 29
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter,V.C. et al. (2001) The sequence of the human genome, Science, 291, 1304-1351.
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, V.C.1
  • 30
    • 0025398721 scopus 로고
    • HATIF: A molecular modelling and drug design program
    • Vriend,G. (1990) HATIF: a molecular modelling and drug design program. J. Mol. Graphics., 8, 52-56.
    • (1990) J. Mol. Graphics. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 31
    • 18444373540 scopus 로고    scopus 로고
    • The Protein Data Bank: Unifying the archive
    • Westbrook,J. et al. (2000) The Protein Data Bank: unifying the archive. Nucleic Acids Res., 30, 245-248.
    • (2000) Nucleic Acids Res. , vol.30 , pp. 245-248
    • Westbrook, J.1
  • 32
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limit of side-chain prediction
    • Xiang,Z. and Honig,B. (2001) Extending the accuracy limit of side-chain prediction. J. Mol. Biol., 311, 421-430.
    • (2001) J. Mol. Biol. , vol.311 , pp. 421-430
    • Xiang, Z.1    Honig, B.2
  • 33
    • 0034663738 scopus 로고    scopus 로고
    • Protein threading using PROSPECT: Design and evaluation
    • Xu,Y. and Xu,D. (2000) Protein threading using PROSPECT: design and evaluation. Protein: Struct. Funct. Genet., 40, 343-354.
    • (2000) Protein: Struct. Funct. Genet. , vol.40 , pp. 343-354
    • Xu, Y.1    Xu, D.2
  • 34
    • 0037852032 scopus 로고    scopus 로고
    • Computational Studies of Protein Structure and Function Using Threading Program PROSPECT
    • Igor Tsigelny (ed.), International University Line Publishers (IUL), La Jolla, CA
    • Xu,D. and Xu,Y. (2002) Computational Studies of Protein Structure and Function Using Threading Program PROSPECT. In Igor Tsigelny (ed.), Protein Structure Prediction: Bioinformatic Approach, International University Line Publishers (IUL), La Jolla, CA, pp. 5-41.
    • (2002) Protein Structure Prediction: Bioinformatic Approach , pp. 5-41
    • Xu, D.1    Xu, Y.2
  • 35
    • 0033677431 scopus 로고    scopus 로고
    • A computational method for NMR-constrained protein threading
    • Xu,Y., Xu,D., Crawford,O. and Einstein,J.R. (2000) A computational method for NMR-constrained protein threading. J. Comput. Biol., 7, 449-467.
    • (2000) J. Comput. Biol. , vol.7 , pp. 449-467
    • Xu, Y.1    Xu, D.2    Crawford, O.3    Einstein, J.R.4
  • 36
    • 0035703315 scopus 로고    scopus 로고
    • Application of PROSPECT in CASP4: Characterizing protein structures with new folds
    • (CASP4 Special Issue)
    • Xu,D., Crawford,O.H., LoCascio,P.F. and Xu,Y. (2001) Application of PROSPECT in CASP4: characterizing protein structures with new folds. Proteins: Struct., Funct. Genet. (CASP4 Special Issue), 46, 140-148.
    • (2001) Proteins: Struct., Funct. Genet , vol.46 , pp. 140-148
    • Xu, D.1    Crawford, O.H.2    LoCascio, P.F.3    Xu, Y.4
  • 37
    • 0035882558 scopus 로고    scopus 로고
    • A model for the three dimensional structure of vitronectin: Predictions for the multi-domain protein from threading and docking
    • Xu,D., Baburaj,K., Peterson,C.B. and Xu,Y. (2001) A model for the three dimensional structure of vitronectin: predictions for the multi-domain protein from threading and docking. Proteins: Struct., Funct. Genet., 44, 312-320.
    • (2001) Proteins: Struct., Funct. Genet. , vol.44 , pp. 312-320
    • Xu, D.1    Baburaj, K.2    Peterson, C.B.3    Xu, Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.