메뉴 건너뛰기




Volumn 7, Issue 3, 1997, Pages 369-376

Population statistics of protein structures: Lessons from structural classifications

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 0030983386     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80054-1     Document Type: Article
Times cited : (145)

References (54)
  • 2
    • 0030200439 scopus 로고    scopus 로고
    • Macromolecular structure information and databases
    • A convenient summary of different protein structure resources, especially those available on the World Wide Web. of special interest
    • Gray PMD, Kemp GJL, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J. Macromolecular structure information and databases. Trends Biochem Sci. 7:1996;251-256 A convenient summary of different protein structure resources, especially those available on the World Wide Web. of special interest.
    • (1996) Trends Biochem Sci , vol.7 , pp. 251-256
    • Gray, P.M.D.1    Kemp, G.J.L.2    Rawlings, C.J.3    Brown, N.P.4    Sander, C.5    Thornton, J.M.6    Orengo, C.M.7    Wodak, S.J.8    Richelle, J.9
  • 3
    • 15844411672 scopus 로고    scopus 로고
    • Extending molecular systematics to the third dimension
    • Wodak SJ. Extending molecular systematics to the third dimension. Nat Struct Biol. 3:1996;575-578.
    • (1996) Nat Struct Biol , vol.3 , pp. 575-578
    • Wodak, S.J.1
  • 4
    • 0028961335 scopus 로고
    • Scop: A structural classification of proteins database for the investigation of sequences and structures
    • This paper introduces the scop database, which hierarchically organizes all proteins of known structure. Scop principally uses manual techniques for domain definition and classification. See also http://scop.mrc-lmb.cam.ac.uk/scop/ of outstanding interest
    • Murzin A, Brenner SE, Hubbard T, Chothia C. Scop: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247:1995;536-540 This paper introduces the scop database, which hierarchically organizes all proteins of known structure. Scop principally uses manual techniques for domain definition and classification. See also http://scop.mrc-lmb.cam.ac.uk/scop/ of outstanding interest.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 5
  • 6
    • 0342982546 scopus 로고    scopus 로고
    • The CATH classification scheme of protein domain structural families
    • A brief announcement of the CATH database, which organizes protein domains into discrete hierarchical levels using a combination of manual and automated techniques, including the SSAP program described in [5]. See also http://www.biochem.ucl.ac.uk/bsm/cath/ of outstanding interest
    • Orengo C, Mitchie A, Jones S, Jones D, Swindells M, Thornton J. The CATH classification scheme of protein domain structural families. Protein Data Bank Quarterly Newsletter. 78:1996;8-9 A brief announcement of the CATH database, which organizes protein domains into discrete hierarchical levels using a combination of manual and automated techniques, including the SSAP program described in [5]. See also http://www.biochem.ucl.ac.uk/bsm/cath/ of outstanding interest.
    • (1996) Protein Data Bank Quarterly Newsletter , vol.78 , pp. 8-9
    • Orengo, C.1    Mitchie, A.2    Jones, S.3    Jones, D.4    Swindells, M.5    Thornton, J.6
  • 7
    • 0030014616 scopus 로고    scopus 로고
    • A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database
    • This paper describes use of the Entrez Structure and the MMDB database, which provides links from each protein to others of similar structure. It is especially valuable because it is part of the larger Entrez system that encompasses protein and nucleic acid sequences and literature references. See also http://www.ncbi.nlm.nih.gov/Structure/ of outstanding interest
    • Hogue CWV, Ohkawa H, Bryant SH. A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem Sci. 1996;226-229 This paper describes use of the Entrez Structure and the MMDB database, which provides links from each protein to others of similar structure. It is especially valuable because it is part of the larger Entrez system that encompasses protein and nucleic acid sequences and literature references. See also http://www.ncbi.nlm.nih.gov/Structure/ of outstanding interest.
    • (1996) Trends Biochem Sci , pp. 226-229
    • Hogue, C.W.V.1    Ohkawa, H.2    Bryant, S.H.3
  • 8
    • 0030765455 scopus 로고    scopus 로고
    • Dali/FSSP classification of three-dimensional protein folds
    • The FSSP database is an automated hierarchical database of structural relationships and is perhaps the most up to date classification. A particularly useful feature is the ability to find structures similar to those of one's own proteins by submitting coordinates to their server. See also http://www.embl-heidelberg.de/dali/fssp/ of outstanding interest
    • Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res. 25:1997;231-234 The FSSP database is an automated hierarchical database of structural relationships and is perhaps the most up to date classification. A particularly useful feature is the ability to find structures similar to those of one's own proteins by submitting coordinates to their server. See also http://www.embl-heidelberg.de/dali/fssp/ of outstanding interest.
    • (1997) Nucleic Acids Res , vol.25 , pp. 231-234
    • Holm, L.1    Sander, C.2
  • 9
    • 0030348027 scopus 로고    scopus 로고
    • A database of globular protein structural domains: Clustering of representative family members into similar folds
    • An automated classification of protein domains. This paper describes the results in useful detail. See also ftp://www.cryst.bbk.ac.uk/pub/ddbase/ of outstanding interest
    • Sowdhamini R, Rufino SD, Blundell TL. A database of globular protein structural domains: clustering of representative family members into similar folds. Fold Des. 1:1996;209-220 An automated classification of protein domains. This paper describes the results in useful detail. See also ftp://www.cryst.bbk.ac.uk/pub/ddbase/ of outstanding interest.
    • (1996) Fold des , vol.1 , pp. 209-220
    • Sowdhamini, R.1    Rufino, S.D.2    Blundell, T.L.3
  • 10
    • 0029950832 scopus 로고    scopus 로고
    • Understanding protein structure: Using scop for fold interpretation
    • How to understand a protein structure in the context of the scop database. The classification of the NAD(P)-binding Rossmann fold domains is explained as an example. of special interest
    • Brenner SE, Chothia C, Hubbard TJP, Murzin AG. Understanding protein structure: using scop for fold interpretation. Methods Enzymol. 266:1996;635-643 How to understand a protein structure in the context of the scop database. The classification of the NAD(P)-binding Rossmann fold domains is explained as an example. of special interest.
    • (1996) Methods Enzymol , vol.266 , pp. 635-643
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.P.3    Murzin, A.G.4
  • 11
    • 0017309766 scopus 로고
    • Structural patterns in globular proteins
    • Levitt M, Chothia C. Structural patterns in globular proteins. Nature. 261:1976;552-557.
    • (1976) Nature , vol.261 , pp. 552-557
    • Levitt, M.1    Chothia, C.2
  • 12
    • 0025753142 scopus 로고
    • Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70kDa heat shock cognate protein
    • Flaherty KM, McKay DB, Kabsch W, Holmes KC. Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70kDa heat shock cognate protein. Proc Natl Acad Sci USA. 88:1991;5041-5045.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 5041-5045
    • Flaherty, K.M.1    McKay, D.B.2    Kabsch, W.3    Holmes, K.C.4
  • 13
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature. 372:1994;631-634.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 14
    • 0027949057 scopus 로고
    • Common structural motifs in small proteins and domains
    • Efimov AV. Common structural motifs in small proteins and domains. FEBS Lett. 355:1994;213-219.
    • (1994) FEBS Lett , vol.355 , pp. 213-219
    • Efimov, A.V.1
  • 15
    • 0030570737 scopus 로고    scopus 로고
    • A structural tree for α-helical proteins containing α-α-corners and its application to protein classification
    • This paper, together with [14], describes a classification of domain structures based on an analysis that is very different from that used in [4,5,6-9,10]. The structure tree is built from the elaboration of a single α-α-corner motif. of outstanding interest of special interest
    • Efimov AV. A structural tree for α-helical proteins containing α-α-corners and its application to protein classification. FEBS Lett. 391:1996;167-170 This paper, together with [14], describes a classification of domain structures based on an analysis that is very different from that used in [4,5,6-9,10]. The structure tree is built from the elaboration of a single α-α-corner motif. of outstanding interest of special interest.
    • (1996) FEBS Lett , vol.391 , pp. 167-170
    • Efimov, A.V.1
  • 16
    • 0025370165 scopus 로고
    • Quantitative organization of the known protein X-ray structures. I. Methods and short-length-scale results
    • Rackovsky S. Quantitative organization of the known protein X-ray structures. I. Methods and short-length-scale results. Proteins. 7:1990;378-402.
    • (1990) Proteins , vol.7 , pp. 378-402
    • Rackovsky, S.1
  • 17
    • 0342982540 scopus 로고
    • Rapid protein-structure classification using one-dimensional structure properties on the bioscan parallel computer
    • Hoffman DL, Laiter S, Singh RK, Vaisman II, Tropsha A. Rapid protein-structure classification using one-dimensional structure properties on the bioscan parallel computer. Comp App Biosci. 11:1995;375-679.
    • (1995) Comp App Biosci , vol.11 , pp. 375-679
    • Hoffman, D.L.1    Laiter, S.2    Singh, R.K.3    Vaisman, I.I.4    Tropsha, A.5
  • 18
    • 0021591646 scopus 로고
    • Recognition of super-secondary structure in proteins
    • Taylor WR, Thornton JM. Recognition of super-secondary structure in proteins. J Mol Biol. 173:1984;487-512.
    • (1984) J Mol Biol , vol.173 , pp. 487-512
    • Taylor, W.R.1    Thornton, J.M.2
  • 20
    • 0026511848 scopus 로고
    • A data bank merging related protein structures and sequences
    • Pascarella S, Argos P. A data bank merging related protein structures and sequences. Protein Eng. 5:1992;121-137.
    • (1992) Protein Eng , vol.5 , pp. 121-137
    • Pascarella, S.1    Argos, P.2
  • 21
    • 0029006864 scopus 로고
    • The alpha-helix as seen from the protein tertiary structure: A 3D structural classification
    • Blundell TL, Zhu ZY. The alpha-helix as seen from the protein tertiary structure: a 3D structural classification. Biophys Chem. 55:1995;167-184.
    • (1995) Biophys Chem , vol.55 , pp. 167-184
    • Blundell, T.L.1    Zhu, Z.Y.2
  • 22
    • 0021844602 scopus 로고
    • β-hairpin families in globular families
    • Sibanda BL, Thornton JM. β-hairpin families in globular families. Nature. 316:1985;170-174.
    • (1985) Nature , vol.316 , pp. 170-174
    • Sibanda, B.L.1    Thornton, J.M.2
  • 23
    • 0030175554 scopus 로고    scopus 로고
    • Discovering protein secondary structure: Classification and description of isolated β-turns
    • Pavone V, Gaeta G, Lombardi A, Nastri F, Maglio O, Isernia C, Saviano M. Discovering protein secondary structure: classification and description of isolated β-turns. Biopolymers. 38:1996;705-721.
    • (1996) Biopolymers , vol.38 , pp. 705-721
    • Pavone, V.1    Gaeta, G.2    Lombardi, A.3    Nastri, F.4    Maglio, O.5    Isernia, C.6    Saviano, M.7
  • 24
    • 0026469666 scopus 로고
    • Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results
    • Prestrelski SJ, Williams AL Jr, Liebman MN. Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results. Proteins. 14:1992;430-439.
    • (1992) Proteins , vol.14 , pp. 430-439
    • Prestrelski, S.J.1    Williams A.L., Jr.2    Liebman, M.N.3
  • 25
    • 0029863769 scopus 로고    scopus 로고
    • Automatic classification and analysis of alpha-alpha-turn motifs in a proteins
    • Wintjens RT, Rooman MJ, Wodak SJ. Automatic classification and analysis of alpha-alpha-turn motifs in a proteins. J Mol Biol. 255:1996;235-253.
    • (1996) J Mol Biol , vol.255 , pp. 235-253
    • Wintjens, R.T.1    Rooman, M.J.2    Wodak, S.J.3
  • 26
    • 0030589039 scopus 로고    scopus 로고
    • Structural families in loops of homologous proteins: Automatic classification, modelling and application to antibodies
    • Martin ACR, Thornton JM. Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. J Mol Biol. 263:1996;800-815.
    • (1996) J Mol Biol , vol.263 , pp. 800-815
    • Martin, A.C.R.1    Thornton, J.M.2
  • 27
    • 0030595337 scopus 로고    scopus 로고
    • Structural classification of HTH DNA - binding domains and protein - DNA interaction modes
    • Wintjens R, Rooman M. Structural classification of HTH DNA - binding domains and protein - DNA interaction modes. J Mol Biol. 262:1996;294-313.
    • (1996) J Mol Biol , vol.262 , pp. 294-313
    • Wintjens, R.1    Rooman, M.2
  • 28
    • 0029096994 scopus 로고
    • Classification of multi-helical DNA-binding domains and applications to predict the DBD structures of σ factor, LysR, OmpR/PhoB, CENP-B, Rap1, and XylS/Ada/AraC
    • Suzuki M, Brenner SE. Classification of multi-helical DNA-binding domains and applications to predict the DBD structures of σ factor, LysR, OmpR/PhoB, CENP-B, Rap1, and XylS/Ada/AraC. FEBS Lett. 372:1995;215-221.
    • (1995) FEBS Lett , vol.372 , pp. 215-221
    • Suzuki, M.1    Brenner, S.E.2
  • 29
    • 0030765155 scopus 로고    scopus 로고
    • Histone and histone fold sequences and structures: A database
    • Baxevanis AD, Landsman D. Histone and histone fold sequences and structures: a database. Nucleic Acids Res. 25:1997;272-273.
    • (1997) Nucleic Acids Res , vol.25 , pp. 272-273
    • Baxevanis, A.D.1    Landsman, D.2
  • 30
    • 0026661145 scopus 로고
    • Selection of a representative set of structures from the Brookhaven Protein Data Bank
    • Boberg J, Salakoski T, Vihinen M. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Proteins. 14:1992;265-276.
    • (1992) Proteins , vol.14 , pp. 265-276
    • Boberg, J.1    Salakoski, T.2    Vihinen, M.3
  • 32
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li H, Helling R, Tang C, Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science. 273:1996;666-669.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 34
    • 0026632379 scopus 로고
    • Predicting protein secondary structure content: A tandem network approach
    • Muskal SM, Kim SH. Predicting protein secondary structure content: a tandem network approach. J Mol Biol. 225:1992;712-727.
    • (1992) J Mol Biol , vol.225 , pp. 712-727
    • Muskal, S.M.1    Kim, S.H.2
  • 35
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • Dubchak I, Muchnik I, Holbrook SR, Kim SH. Prediction of protein folding class using global description of amino acid sequence. Proc Natl Acad Sci USA. 92:1992;8700-8704.
    • (1992) Proc Natl Acad Sci USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchnik, I.2    Holbrook, S.R.3    Kim, S.H.4
  • 36
    • 0030814427 scopus 로고    scopus 로고
    • An update of the DEF database of protein fold class predictions
    • Reczko M, Karras D, Bohr H. An update of the DEF database of protein fold class predictions. Nucleic Acids Res. 25:1997;235.
    • (1997) Nucleic Acids Res , vol.25 , pp. 235
    • Reczko, M.1    Karras, D.2    Bohr, H.3
  • 37
    • 0028906598 scopus 로고
    • Neural networks for secondary structure and structural class predictions
    • Chandonia JM, Karplus M. Neural networks for secondary structure and structural class predictions. Protein Sci. 4:1995;275-285.
    • (1995) Protein Sci , vol.4 , pp. 275-285
    • Chandonia, J.M.1    Karplus, M.2
  • 38
    • 0029051959 scopus 로고
    • A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space
    • Chou KC. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins. 21:1995;319-344.
    • (1995) Proteins , vol.21 , pp. 319-344
    • Chou, K.C.1
  • 39
    • 0030595369 scopus 로고    scopus 로고
    • Analysis of domain structural class using an automated class assignment protocol
    • An in-depth survey of the structural principles that define classes, and a test of the ability of automated procedures to identify them. This paper also investigates nonstructural characteristics of proteins in the different classes of special interest
    • Mitchie AD, Orengo CA, Thornton JM. Analysis of domain structural class using an automated class assignment protocol. J Mol Biol. 262:1996;168-185 An in-depth survey of the structural principles that define classes, and a test of the ability of automated procedures to identify them. This paper also investigates nonstructural characteristics of proteins in the different classes of special interest.
    • (1996) J Mol Biol , vol.262 , pp. 168-185
    • Mitchie, A.D.1    Orengo, C.A.2    Thornton, J.M.3
  • 40
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • A broad survey of known protein structures, which introduces the concept of five attractors as very common protein architectural frameworks. of special interest
    • Holm L, Sander C. Mapping the protein universe. Science. 273:1996;595-602 A broad survey of known protein structures, which introduces the concept of five attractors as very common protein architectural frameworks. of special interest.
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 41
    • 0016368465 scopus 로고
    • Computer analysis of protein sequences
    • Dayhoff MO. Computer analysis of protein sequences. Feder Proc. 33:1974;2314-2316.
    • (1974) Feder Proc , vol.33 , pp. 2314-2316
    • Dayhoff, M.O.1
  • 42
    • 0016729111 scopus 로고
    • The appearance of new structures and functions in proteins during evolution
    • Zuckerkandl E. The appearance of new structures and functions in proteins during evolution. J Mol Evol. 7:1975;1-57.
    • (1975) J Mol Evol , vol.7 , pp. 1-57
    • Zuckerkandl, E.1
  • 43
    • 0027122748 scopus 로고
    • One thousand families for the molecular biologist
    • Chothia C. One thousand families for the molecular biologist. Nature. 357:1992;543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 44
    • 0031020765 scopus 로고    scopus 로고
    • How far can sequences diverge?
    • Chothia C, Gerstein M. How far can sequences diverge? Nature. 385:1997;579-580.
    • (1997) Nature , vol.385 , pp. 579-580
    • Chothia, C.1    Gerstein, M.2
  • 45
    • 0028825575 scopus 로고
    • Ahead of schedule and under budget: The genome project passes its fifth birthday
    • Collins FS. Ahead of schedule and under budget: the genome project passes its fifth birthday. Proc Natl Acad Sci USA. 92:1995;10821-10823.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 10821-10823
    • Collins, F.S.1
  • 46
    • 0028818340 scopus 로고
    • Protein structure prediction by threading methods: Evaluation of current techniques
    • Lemer CM-R, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current techniques. Proteins. 23:1995;337-355.
    • (1995) Proteins , vol.23 , pp. 337-355
    • Lemer, C.-R.1    Rooman, M.J.2    Wodak, S.J.3
  • 47
    • 0029008017 scopus 로고    scopus 로고
    • Statistics of sequence - structure threading
    • Bryant SH, Altschul SF. Statistics of sequence - structure threading. Curr Opin Struct Biol. 5:1996;236-244.
    • (1996) Curr Opin Struct Biol , vol.5 , pp. 236-244
    • Bryant, S.H.1    Altschul, S.F.2
  • 48
    • 0030067191 scopus 로고    scopus 로고
    • Assigning amino acid sequences to 3-dimensional protein folds
    • Fischer D, Rice D, Bowie JU, Eisenberg D. Assigning amino acid sequences to 3-dimensional protein folds. FASEB J. 10:1996;126-136.
    • (1996) FASEB J , vol.10 , pp. 126-136
    • Fischer, D.1    Rice, D.2    Bowie, J.U.3    Eisenberg, D.4
  • 49
    • 0029937428 scopus 로고    scopus 로고
    • Hidden Markov models
    • Eddy SR. Hidden Markov models. Curr Opin Struct Biol. 6:1996;356-361.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 356-361
    • Eddy, S.R.1
  • 50
    • 0029665409 scopus 로고    scopus 로고
    • Identification of sequence patterns with profile analysis
    • Gribskov M, Veretnik S. Identification of sequence patterns with profile analysis. Methods Enzymol. 266:1996;198-211.
    • (1996) Methods Enzymol , vol.266 , pp. 198-211
    • Gribskov, M.1    Veretnik, S.2
  • 52
    • 0029950031 scopus 로고    scopus 로고
    • Structural classification of proteins: New superfamilies
    • Murzin AG. Structural classification of proteins: new superfamilies. Curr Opin Struct Biol. 6:1996;386-394.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 386-394
    • Murzin, A.G.1
  • 53
    • 0027176843 scopus 로고
    • Polypeptide folding of Bacillus cereus ATCC7064 oligo-1,6-glucosidase revealed by 3.0 Å resolution X-ray analysis
    • Kizaki H, Hata Y, Watanabe K, Katsube Y, Suzuki Y. Polypeptide folding of Bacillus cereus ATCC7064 oligo-1,6-glucosidase revealed by 3.0 Å resolution X-ray analysis. J Biochem (Tokyo). 113:1993;646-649.
    • (1993) J Biochem (Tokyo) , vol.113 , pp. 646-649
    • Kizaki, H.1    Hata, Y.2    Watanabe, K.3    Katsube, Y.4    Suzuki, Y.5
  • 54
    • 0013675412 scopus 로고    scopus 로고
    • Molecular proprinquity: Evolutionary and structural relationships of proteins
    • Cambridge: Cambridge University
    • Brenner SE. Molecular proprinquity: evolutionary and structural relationships of proteins. PhD Thesis. 1996;Cambridge University, Cambridge.
    • (1996) PhD Thesis
    • Brenner, S.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.