메뉴 건너뛰기




Volumn , Issue , 2005, Pages 365-385

Identifying Structural Domains in Proteins

Author keywords

First generation algorithms; Sequence patterns; Structural domains in proteins

Indexed keywords

FIRST-GENERATION ALGORITHMS; SEQUENCE PATTERNS; STRUCTURAL DOMAINS;

EID: 84880135206     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471721204.ch18     Document Type: Chapter
Times cited : (3)

References (60)
  • 1
    • 0025350086 scopus 로고
    • An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion
    • Argos P (1990): An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. J Mol Biol 211:943-58.
    • (1990) J Mol Biol , vol.211 , pp. 943-958
    • Argos, P.1
  • 3
    • 0028204771 scopus 로고
    • Domain swapping: entangling alliances between proteins
    • [The original paper describing the domain swapping principle and suggesting it as a general principle for the evolution of multimeric proteins.]
    • Bennett MJ, Choe S, Eisenberg D (1994): Domain swapping: entangling alliances between proteins. Proc Natl Acad Sci USA 91:3127-31. [The original paper describing the domain swapping principle and suggesting it as a general principle for the evolution of multimeric proteins.]
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 3127-3131
    • Bennett, M.J.1    Choe, S.2    Eisenberg, D.3
  • 6
    • 0030983386 scopus 로고    scopus 로고
    • Population statistics of protein structures: lessons from structural classifications
    • Brenner SE, Chothia C, Hubbard TJ (1997): Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol 7:369-76.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 369-376
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 7
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • [Before any complete genome sequences was available, this short note presents arguments in support of the idea that the number of protein folds shared by all organisms is limited to about 1000.]
    • Chothia C (1992): Proteins. One thousand families for the molecular biologist. Nature 357:543-4. [Before any complete genome sequences was available, this short note presents arguments in support of the idea that the number of protein folds shared by all organisms is limited to about 1000.]
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 8
    • 0028356670 scopus 로고
    • The thermodynamics of the unfolding of an isolated protein subdomain. The 255-316 C-terminal fragment of thermolysin
    • Conejero-Lara F, De Filippis V, Fontana A, Mateo PL (1994): The thermodynamics of the unfolding of an isolated protein subdomain. The 255-316 C-terminal fragment of thermolysin. FEBS Lett 344:154-6.
    • (1994) FEBS Lett , vol.344 , pp. 154-156
    • Conejero-Lara, F.1    De Filippis, V.2    Fontana, A.3    Mateo, P.L.4
  • 9
    • 0034601917 scopus 로고    scopus 로고
    • Homology among (βα/8) barrels: implications for the evolution of metabolic pathways
    • Copley RR, Bork P (2000): Homology among (βα/8) barrels: implications for the evolution of metabolic pathways. J Mol Biol 303:627-41.
    • (2000) J Mol Biol , vol.303 , pp. 627-641
    • Copley, R.R.1    Bork, P.2
  • 10
    • 0033957841 scopus 로고    scopus 로고
    • ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons
    • Corpet F, Servant F, Gouzy J, Kahn D (2000): ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res 28:267-9.
    • (2000) Nucleic Acids Res , vol.28 , pp. 267-269
    • Corpet, F.1    Servant, F.2    Gouzy, J.3    Kahn, D.4
  • 11
    • 0018270134 scopus 로고
    • The tree structural organization of proteins
    • [One of the very first systematic procedure for identifying structural domains in proteins.]
    • Crippen GM (1978): The tree structural organization of proteins. J Mol Biol 126:315-32. [One of the very first systematic procedure for identifying structural domains in proteins.]
    • (1978) J Mol Biol , vol.126 , pp. 315-332
    • Crippen, G.M.1
  • 12
    • 0029006062 scopus 로고
    • The multiplicity of domains in proteins
    • Doolittle RF (1995): The multiplicity of domains in proteins. Ann Rev Biochem 64:287-314.
    • (1995) Ann Rev Biochem , vol.64 , pp. 287-314
    • Doolittle, R.F.1
  • 13
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999): Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-90.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 14
    • 0028355575 scopus 로고
    • The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes
    • Fani R, Lio P, Chiarelli I, Bazzicalupo M (1994): The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. J Mol Evol 38:489-95.
    • (1994) J Mol Evol , vol.38 , pp. 489-495
    • Fani, R.1    Lio, P.2    Chiarelli, I.3    Bazzicalupo, M.4
  • 15
    • 0035895514 scopus 로고    scopus 로고
    • Proteomics. Proteomics in genomeland
    • Fields S (2001): Proteomics. Proteomics in genomeland. Science 291:1221-4.
    • (2001) Science , vol.291 , pp. 1221-1224
    • Fields, S.1
  • 16
    • 0020742670 scopus 로고
    • Modular structural units, exons, and function in chicken lysozyme
    • Go M (1983): Modular structural units, exons, and function in chicken lysozyme. Proc Natl Acad Sci USA 80:1964-8.
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 1964-1968
    • Go, M.1
  • 17
    • 0031857779 scopus 로고    scopus 로고
    • Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities
    • Gracy J, Argos P (1998): Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities. Bioinformatics 14:174-87.
    • (1998) Bioinformatics , vol.14 , pp. 174-187
    • Gracy, J.1    Argos, P.2
  • 19
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • [The first truly general algorithm for defining structural domains that can identify domains comprising multiple chain segments.]
    • Holm L, Sander C (1994): Parser for protein folding units. Proteins 19:256-68. [The first truly general algorithm for defining structural domains that can identify domains comprising multiple chain segments.]
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 20
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L, Sander C (1996): Mapping the protein universe. Science 273:595-603.
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 21
    • 0028891784 scopus 로고
    • Identification and analysis of domains in proteins
    • Islam SA, Luo J, Sternberg MJ (1995): Identification and analysis of domains in proteins. Protein Eng 8:513-25.
    • (1995) Protein Eng , vol.8 , pp. 513-525
    • Islam, S.A.1    Luo, J.2    Sternberg, M.J.3
  • 22
    • 0020655246 scopus 로고
    • Structural domains in proteins and their role in the dynamics of protein function
    • Janin J, Wodak SJ (1983): Structural domains in proteins and their role in the dynamics of protein function. Prog Biophys Mol Biol 42:21-78.
    • (1983) Prog Biophys Mol Biol , vol.42 , pp. 21-78
    • Janin, J.1    Wodak, S.J.2
  • 23
    • 0031889752 scopus 로고    scopus 로고
    • Domain assignment for protein structures using a consensus approach: characterization and analysis
    • [A useful systematic comparison between different methods for assigning structural domains in proteins.]
    • Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM (1998): Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci 7:233-42. [A useful systematic comparison between different methods for assigning structural domains in proteins.]
    • (1998) Protein Sci , vol.7 , pp. 233-242
    • Jones, S.1    Stewart, M.2    Michie, A.3    Swindells, M.B.4    Orengo, C.5    Thornton, J.M.6
  • 24
    • 0034060520 scopus 로고    scopus 로고
    • Protein domain interfaces: characterization and comparison with oligomeric protein interfaces
    • Jones S, Marin A, Thornton JM (2000): Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Eng 13:77-82.
    • (2000) Protein Eng , vol.13 , pp. 77-82
    • Jones, S.1    Marin, A.2    Thornton, J.M.3
  • 25
    • 84990479742 scopus 로고
    • An efficient heuristic procedure for partitioning graphs
    • Kernighan BW (1970): An efficient heuristic procedure for partitioning graphs. Bell Systems Tech J 49:291-307.
    • (1970) Bell Systems Tech J , vol.49 , pp. 291-307
    • Kernighan, B.W.1
  • 26
    • 0024057934 scopus 로고
    • Prediction of the location of structural domains in globular proteins
    • Kikuchi T, Nemethy G, Scheraga HA (1988): Prediction of the location of structural domains in globular proteins. J Protein Chem 7:427-71.
    • (1988) J Protein Chem , vol.7 , pp. 427-471
    • Kikuchi, T.1    Nemethy, G.2    Scheraga, H.A.3
  • 29
    • 0032921818 scopus 로고    scopus 로고
    • Structural genomics: keystone for a human proteome project
    • Montelione GT, Anderson S (1999): Structural genomics: keystone for a human proteome project. Nat Struct Biol 6:11-2.
    • (1999) Nat Struct Biol , vol.6 , pp. 11-12
    • Montelione, G.T.1    Anderson, S.2
  • 30
    • 0025906759 scopus 로고
    • An analysis of protein folding pathways
    • Moult J, Unger R (1991): An analysis of protein folding pathways. Biochemistry 30:3816-24.
    • (1991) Biochemistry , vol.30 , pp. 3816-3824
    • Moult, J.1    Unger, R.2
  • 31
    • 0034491151 scopus 로고    scopus 로고
    • A simple probabilistic scoring method for protein domain identification
    • Murvai J, Vlahovicek K, Pongor S (2000): A simple probabilistic scoring method for protein domain identification. Bioinformatics 16:1155-6.
    • (2000) Bioinformatics , vol.16 , pp. 1155-1156
    • Murvai, J.1    Vlahovicek, K.2    Pongor, S.3
  • 32
    • 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 (1995): SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-40.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 34
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo CA, Jones DT, Thornton JM (1994): Protein superfamilies and domain superfolds. Nature 372:631-4.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 36
    • 0006233908 scopus 로고
    • Past and present
    • In: Goodwin TW, editors., London:Academic Press, [The pioneering study in which the idea of structural domains was first described.]
    • Phillips DC (1970): Past and present. In: Goodwin TW, editors. British Biochemistry London:Academic Press, pp 11-28. [The pioneering study in which the idea of structural domains was first described.]
    • (1970) British Biochemistry , pp. 11-28
    • Phillips, D.C.1
  • 37
    • 0015834475 scopus 로고
    • Comparison of super-secondary structures in proteins
    • Rao ST, Rossmann MG (1973): Comparison of super-secondary structures in proteins. J Mol Biol 76:241-56.
    • (1973) J Mol Biol , vol.76 , pp. 241-256
    • Rao, S.T.1    Rossmann, M.G.2
  • 38
    • 0019874608 scopus 로고
    • Location of domains in globular proteins
    • Rashin AA (1981): Location of domains in globular proteins. Nature 291:85-7.
    • (1981) Nature , vol.291 , pp. 85-87
    • Rashin, A.A.1
  • 39
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS (1981): The anatomy and taxonomy of protein structure. Adv Protein Chem 34:167-339.
    • (1981) Adv Protein Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 40
    • 0018782641 scopus 로고
    • Hierarchic organization of domains in globular proteins
    • [One of the first systematic procedures for defining structural domains in proteins from the atomic coordinates.]
    • Rose GD (1979): Hierarchic organization of domains in globular proteins. J Mol Biol 134:447-70. [One of the first systematic procedures for defining structural domains in proteins from the atomic coordinates.]
    • (1979) J Mol Biol , vol.134 , pp. 447-470
    • Rose, G.D.1
  • 41
    • 0016255253 scopus 로고
    • Letter: Recognition of structural domains in globular proteins
    • [One of the pioneering studies in which the idea of structural domains was first described.]
    • Rossman MG, Liljas A (1974): Letter: Recognition of structural domains in globular proteins. J Mol Biol 85:177-81. [One of the pioneering studies in which the idea of structural domains was first described.]
    • (1974) J Mol Biol , vol.85 , pp. 177-181
    • Rossman, M.G.1    Liljas, A.2
  • 42
    • 0022977712 scopus 로고
    • A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps
    • Sadowski I, Stone JC, Pawson T (1986): A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. Mol Cell Biol 6:4396-408.
    • (1986) Mol Cell Biol , vol.6 , pp. 4396-4408
    • Sadowski, I.1    Stone, J.C.2    Pawson, T.3
  • 44
    • 0028943588 scopus 로고
    • Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions
    • Siddiqui AS, Barton GJ (1995): Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci 4:872-84.
    • (1995) Protein Sci , vol.4 , pp. 872-884
    • Siddiqui, A.S.1    Barton, G.J.2
  • 45
    • 0028914725 scopus 로고
    • An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins
    • Sowdhamini R, Blundell TL (1995): An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci 4:506-20.
    • (1995) Protein Sci , vol.4 , pp. 506-520
    • Sowdhamini, R.1    Blundell, T.L.2
  • 47
    • 0028937153 scopus 로고
    • A procedure for detecting structural domains in proteins
    • Swindells MB (1995a) A procedure for detecting structural domains in proteins. Protein Sci 4:103-12.
    • (1995) Protein Sci , vol.4 , pp. 103-112
    • Swindells, M.B.1
  • 48
    • 0028907319 scopus 로고
    • A procedure for the automatic determination of hydrophobic cores in protein structures
    • Swindells MB (1995b) A procedure for the automatic determination of hydrophobic cores in protein structures. Protein Sci 4:93-102.
    • (1995) Protein Sci , vol.4 , pp. 93-102
    • Swindells, M.B.1
  • 49
    • 0032951163 scopus 로고    scopus 로고
    • Protein structural domain identification
    • [An elegant heuristic procedure, inspired by the Ising model of solid-state physics, for assigning structural domains in proteins.]
    • Taylor WR (1999): Protein structural domain identification. Protein Eng 12:203-16. [An elegant heuristic procedure, inspired by the Ising model of solid-state physics, for assigning structural domains in proteins.]
    • (1999) Protein Eng , vol.12 , pp. 203-216
    • Taylor, W.R.1
  • 50
    • 0032211977 scopus 로고    scopus 로고
    • A histidine gene cluster of the hyperthermophile Thermotoga maritima: sequence analysis and evolutionary significance
    • Thoma R, Schwander M, Liebl W, Kirschner K, Sterner R (1998): A histidine gene cluster of the hyperthermophile Thermotoga maritima: sequence analysis and evolutionary significance. Extremophiles 2:379-89.
    • (1998) Extremophiles , vol.2 , pp. 379-389
    • Thoma, R.1    Schwander, M.2    Liebl, W.3    Kirschner, K.4    Sterner, R.5
  • 51
    • 0033780375 scopus 로고    scopus 로고
    • Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion
    • Tsoka S, Ouzounis CA (2000): Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat Genet 26:141-2.
    • (2000) Nat Genet , vol.26 , pp. 141-142
    • Tsoka, S.1    Ouzounis, C.A.2
  • 52
    • 0033562691 scopus 로고    scopus 로고
    • Identification of structural domains in proteins by a graph heuristic
    • [This paper describes a novel graph theoretical procedure for assigning structural domains in proteins. Handles any number of noncontiguous chain segments, uses no information on secondary structure. A discriminant analysis is used to derive a set of criteria that define physically meaningful domains.]
    • Wernisch L, Hunting M, Wodak SJ (1999): Identification of structural domains in proteins by a graph heuristic. Proteins 35:338-52. [This paper describes a novel graph theoretical procedure for assigning structural domains in proteins. Handles any number of noncontiguous chain segments, uses no information on secondary structure. A discriminant analysis is used to derive a set of criteria that define physically meaningful domains.]
    • (1999) Proteins , vol.35 , pp. 338-352
    • Wernisch, L.1    Hunting, M.2    Wodak, S.J.3
  • 53
    • 0015597839 scopus 로고
    • Nucleation, rapid folding, and globular intrachain regions in proteins
    • The first definition and systematic analysis of structural domains in proteins.]
    • Wetlaufer DB (1973): Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 70:697-701. The first definition and systematic analysis of structural domains in proteins.]
    • (1973) Proc Natl Acad Sci USA , vol.70 , pp. 697-701
    • Wetlaufer, D.B.1
  • 54
    • 0033753811 scopus 로고    scopus 로고
    • Domain size distributions can predict domain boundaries
    • [One of the few attempts to define structural domains from sequence information.]
    • Wheelan SJ, Marchler-Bauer A, Bryant SH (2000): Domain size distributions can predict domain boundaries. Bioinformatics 16:613-8. [One of the few attempts to define structural domains from sequence information.]
    • (2000) Bioinformatics , vol.16 , pp. 613-618
    • Wheelan, S.J.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 55
    • 85080342193 scopus 로고
    • Defining compact domains in globular proteins
    • In Balaban M. editors., Rehovot: Israel International Science Services, [One of the first approaches for identifying small, compact substructures in proteins that are likely to be stable.]
    • Wodak SJ, Janin J (1981a) Defining compact domains in globular proteins. In Balaban M. editors. Structural Aspects of Recognition and Assembly in Biological Macromolecules. Rehovot: Israel International Science Services, pp 149-67. [One of the first approaches for identifying small, compact substructures in proteins that are likely to be stable.]
    • (1981) Structural Aspects of Recognition and Assembly in Biological Macromolecules , pp. 149-167
    • Wodak, S.J.1    Janin, J.2
  • 56
    • 0019877668 scopus 로고
    • Location of structural domains in protein
    • [This paper describes the first approach for defining structural domains in proteins that relies on the evaluation of some physical property (size of the domain interface) as opposed to purely geometric criteria.]
    • Wodak SJ, Janin J (1981b) Location of structural domains in protein. Biochemistry 20:6544-52. [This paper describes the first approach for defining structural domains in proteins that relies on the evaluation of some physical property (size of the domain interface) as opposed to purely geometric criteria.]
    • (1981) Biochemistry , vol.20 , pp. 6544-6552
    • Wodak, S.J.1    Janin, J.2
  • 57
    • 0034491038 scopus 로고    scopus 로고
    • Protein domain decomposition using a graph-theoretic approach
    • Xu Y, Xu D, Gabow HN (2000): Protein domain decomposition using a graph-theoretic approach. Bioinformatics 16:1091-104.
    • (2000) Bioinformatics , vol.16 , pp. 1091-1104
    • Xu, Y.1    Xu, D.2    Gabow, H.N.3
  • 58
    • 0033800628 scopus 로고    scopus 로고
    • A new method for protein domain recognition
    • Xuan ZY, Ling LJ, Chen RS (2000): A new method for protein domain recognition. Eur Biophys J 29:7-16.
    • (2000) Eur Biophys J , vol.29 , pp. 7-16
    • Xuan, Z.Y.1    Ling, L.J.2    Chen, R.S.3
  • 59
    • 0027953575 scopus 로고
    • Binary discontinuous compact protein domains
    • Zehfus MH (1994): Binary discontinuous compact protein domains. Protein Eng 7:335-40.
    • (1994) Protein Eng , vol.7 , pp. 335-340
    • Zehfus, M.H.1
  • 60
    • 0023055758 scopus 로고
    • Compact units in proteins
    • Zehfus MH, Rose GD (1986): Compact units in proteins. Biochemistry 25:5759-65.
    • (1986) Biochemistry , vol.25 , pp. 5759-5765
    • Zehfus, M.H.1    Rose, G.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.