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Volumn 64, Issue 3, 2006, Pages 601-614

Dynamic domain threading

Author keywords

Decoy models; Domain definition; Protein modeling

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE;

EID: 33746268462     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20915     Document Type: Article
Times cited : (12)

References (39)
  • 1
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force, an approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. Calculation of conformational ensembles from potentials of mean force, an approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 2
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 3
    • 0025341237 scopus 로고
    • Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
    • Bowie JU, Clarke ND, Pabo CO, Sauer RT. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins 1990;7:257-264.
    • (1990) Proteins , vol.7 , pp. 257-264
    • Bowie, J.U.1    Clarke, N.D.2    Pabo, C.O.3    Sauer, R.T.4
  • 4
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Lüthy, R.2    Eisenberg, D.3
  • 6
    • 0022550940 scopus 로고
    • Identification of protein sequence homology by consensus template alignment
    • Taylor WR. Identification of protein sequence homology by consensus template alignment. J Mol Biol 1986;188:233-258.
    • (1986) J Mol Biol , vol.188 , pp. 233-258
    • Taylor, W.R.1
  • 7
    • 0031588007 scopus 로고    scopus 로고
    • Multiple sequence threading: An analysis of alignment quality and stability
    • Taylor WR. Multiple sequence threading: an analysis of alignment quality and stability. J Mol Biol 1997;269:902-943.
    • (1997) J Mol Biol , vol.269 , pp. 902-943
    • Taylor, W.R.1
  • 8
    • 0033200307 scopus 로고
    • A systematic comparison of protein structure classifications SCOP, CATH and FSSP
    • Hadley C, Jones DT. A systematic comparison of protein structure classifications SCOP, CATH and FSSP. Structure 1995;7:1099-1112.
    • (1995) Structure , vol.7 , pp. 1099-1112
    • Hadley, C.1    Jones, D.T.2
  • 9
    • 0029119568 scopus 로고
    • RasMol: Biomolecular graphics for all
    • Sayle R, Milner-White EJ. RasMol: Biomolecular graphics for all. TIBS 1995;20:374-375.
    • (1995) TIBS , vol.20 , pp. 374-375
    • Sayle, R.1    Milner-White, E.J.2
  • 10
    • 0032951163 scopus 로고    scopus 로고
    • Protein structure domain identification
    • Taylor WR. Protein structure domain identification. Prot Eng 1999;12:203-216.
    • (1999) Prot Eng , vol.12 , pp. 203-216
    • Taylor, W.R.1
  • 12
    • 0024097647 scopus 로고
    • Data-sieving hydrophobicity plots
    • Bangham JA. Data-sieving hydrophobicity plots. Anal Biochem 1988;174:142-145.
    • (1988) Anal Biochem , vol.174 , pp. 142-145
    • Bangham, J.A.1
  • 13
    • 0035958742 scopus 로고    scopus 로고
    • Defining linear segments in protein structure
    • Taylor WR. Defining linear segments in protein structure. J Mol Biol 2001;310:1135-1150.
    • (2001) J Mol Biol , vol.310 , pp. 1135-1150
    • Taylor, W.R.1
  • 14
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000;16:404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • Jones, D.T.1
  • 16
    • 0036639910 scopus 로고    scopus 로고
    • Parameter optimized surfaces (POPS): Analysis of key interactions and conformational changes in the ribosome
    • Fraternali F, Cavallo L. Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Res 2002;30:2950-2960.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2950-2960
    • Fraternali, F.1    Cavallo, L.2
  • 17
    • 0042121261 scopus 로고    scopus 로고
    • POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level
    • Cavallo L, Kleinjung J, Fraternali F. POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res 2003;31:3364-3366.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3364-3366
    • Cavallo, L.1    Kleinjung, J.2    Fraternali, F.3
  • 18
    • 0030825816 scopus 로고    scopus 로고
    • Residual colours: A proposal for aminochromography
    • Taylor WR. Residual colours: a proposal for aminochromography. Prot Eng 1997;10:743-746.
    • (1997) Prot Eng , vol.10 , pp. 743-746
    • Taylor, W.R.1
  • 19
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comp Appl Biol Sci 1992;8:275-282.
    • (1992) Comp Appl Biol Sci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 20
  • 21
    • 0038348418 scopus 로고    scopus 로고
    • Ab initio modelling of the N-terminal domain of the secretin receptors
    • Taylor WR, Munro REJ, Petersen K, Bywater RP. Ab initio modelling of the N-terminal domain of the secretin receptors. Comp Biol Chem 2003;27:103-114.
    • (2003) Comp Biol Chem , vol.27 , pp. 103-114
    • Taylor, W.R.1    Munro, R.E.J.2    Petersen, K.3    Bywater, R.P.4
  • 22
    • 0028166611 scopus 로고
    • Folding polypeptide α-carbon backbones by distance geometry methods
    • Aszódi A, Taylor WR. Folding polypeptide α-carbon backbones by distance geometry methods. Biopolymers 1994;34:489-506.
    • (1994) Biopolymers , vol.34 , pp. 489-506
    • Aszódi, A.1    Taylor, W.R.2
  • 23
    • 0037474530 scopus 로고    scopus 로고
    • Modelling zinc-binding proteins with GADGET: Genetic algorithm and distance geometry for exploring topology
    • Petersen K, Taylor WR. Modelling zinc-binding proteins with GADGET: Genetic algorithm and distance geometry for exploring topology. J Mol Biol 2003;325:1039-1059.
    • (2003) J Mol Biol , vol.325 , pp. 1039-1059
    • Petersen, K.1    Taylor, W.R.2
  • 24
    • 0025269891 scopus 로고
    • Novel method for the rapid evaluation of packing in protein structures
    • Gregoret LM, Cohen FE. Novel method for the rapid evaluation of packing in protein structures. J Mol Biol 1990;211:959-974.
    • (1990) J Mol Biol , vol.211 , pp. 959-974
    • Gregoret, L.M.1    Cohen, F.E.2
  • 25
    • 0034710671 scopus 로고    scopus 로고
    • A deeply knotted protein and how it might fold
    • Taylor WR. A deeply knotted protein and how it might fold. Nature 2000;406:916-919.
    • (2000) Nature , vol.406 , pp. 916-919
    • Taylor, W.R.1
  • 26
    • 0036772706 scopus 로고    scopus 로고
    • Threading using neural networks (TUNE): The measure of protein sequence-structure compatibility
    • Lin K, May AC, Taylor WR. Threading using neural networks (TUNE): the measure of protein sequence-structure compatibility. Bioinformatics 2002;18:1350-1357.
    • (2002) Bioinformatics , vol.18 , pp. 1350-1357
    • Lin, K.1    May, A.C.2    Taylor, W.R.3
  • 27
    • 0026723852 scopus 로고
    • Use of a potential of mean force to analyze free-energy contributions in protein folding
    • Avbelj F. Use of a potential of mean force to analyze free-energy contributions in protein folding. Biochemistry 1992;31:6290-6297.
    • (1992) Biochemistry , vol.31 , pp. 6290-6297
    • Avbelj, F.1
  • 28
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916.
    • (1998) J Mol Biol , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 29
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Prot Struct Funct Genet 2001;44:223-232, 2001.
    • (2001) Prot Struct Funct Genet , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 30
    • 3042726390 scopus 로고    scopus 로고
    • A structural pattern-based method for protein fold recognition
    • Taylor WR, Jonassen I. A structural pattern-based method for protein fold recognition. Proteins 2004;56:222-234.
    • (2004) Proteins , vol.56 , pp. 222-234
    • Taylor, W.R.1    Jonassen, I.2
  • 31
    • 0033081985 scopus 로고    scopus 로고
    • Discovery of local packing motifs in protein structures
    • Jonassen I, Eidhammer I, Taylor WR. Discovery of local packing motifs in protein structures. Proteins 1999;34:206-219.
    • (1999) Proteins , vol.34 , pp. 206-219
    • Jonassen, I.1    Eidhammer, I.2    Taylor, W.R.3
  • 33
    • 0034623980 scopus 로고    scopus 로고
    • Searching the protein structure databank with weak sequence patterns and structural constraints
    • Jonassen I, Eidhammer I, Grindhaug SH, Taylor WR. Searching the protein structure databank with weak sequence patterns and structural constraints. J Mol Biol 2000;304:599-619.
    • (2000) J Mol Biol , vol.304 , pp. 599-619
    • Jonassen, I.1    Eidhammer, I.2    Grindhaug, S.H.3    Taylor, W.R.4
  • 34
    • 0030765455 scopus 로고    scopus 로고
    • Dali/FSSP classification of three-dimensional protein folds
    • Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997;25:231-234.
    • (1997) Nucleic Acids Res , vol.25 , pp. 231-234
    • Holm, L.1    Sander, C.2
  • 35
    • 0033011876 scopus 로고    scopus 로고
    • Protein structure alignment using iterated double dynamic programming
    • Taylor WR. Protein structure alignment using iterated double dynamic programming. Prot Sci 1999;8:654-665.
    • (1999) Prot Sci , vol.8 , pp. 654-665
    • Taylor, W.R.1
  • 38
    • 2942514454 scopus 로고    scopus 로고
    • Consensus molecular models for the amino terminal domain of the retrovirus restriction gene fv1 and the murine leukaemia virus capsid proteins
    • Taylor WR, Stoye JP. Consensus molecular models for the amino terminal domain of the retrovirus restriction gene fv1 and the murine leukaemia virus capsid proteins. JMC Struct Biol 2004;4:1-15.
    • (2004) JMC Struct Biol , vol.4 , pp. 1-15
    • Taylor, W.R.1    Stoye, J.P.2
  • 39
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287:797-815.
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.