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Volumn 8, Issue 1, 2004, Pages 3-7

Searching for functional sites in protein structures

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 1042264059     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2003.11.001     Document Type: Review
Times cited : (136)

References (42)
  • 1
    • 0033757822 scopus 로고    scopus 로고
    • An overview of structural genomics
    • Burley S.K. An overview of structural genomics. Nat Struct Biol. 7:2000;932-934.
    • (2000) Nat Struct Biol , vol.7 , pp. 932-934
    • Burley, S.K.1
  • 3
    • 0034753838 scopus 로고    scopus 로고
    • Identification of homology in protein structure classification
    • Dietmann S., Holm L. Identification of homology in protein structure classification. Nat Struct Biol. 8:2001;953-957.
    • (2001) Nat Struct Biol , vol.8 , pp. 953-957
    • Dietmann, S.1    Holm, L.2
  • 4
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo C.A., Jones D., Thornton J.M. Protein superfamilies and domain superfolds. Nature. 372:1994;631-634.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.2    Thornton, J.M.3
  • 5
    • 0032859140 scopus 로고    scopus 로고
    • Evolution of protein function, from a structural perspective
    • Todd A.E., Orengo C.A., Thornton J.M. Evolution of protein function, from a structural perspective. Curr Opin Chem Biol. 3:1999;548-556.
    • (1999) Curr Opin Chem Biol , vol.3 , pp. 548-556
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 8
    • 0037424601 scopus 로고    scopus 로고
    • A model for statistical significance of local similarities in structure
    • A new method to calculate the statistical significance of the RMSD between common local patterns in protein structures.
    • Stark A., Sunyaev S., Russell R.B. A model for statistical significance of local similarities in structure. J Mol Biol. 326:2003;1307-1316 A new method to calculate the statistical significance of the RMSD between common local patterns in protein structures.
    • (2003) J Mol Biol , vol.326 , pp. 1307-1316
    • Stark, A.1    Sunyaev, S.2    Russell, R.B.3
  • 9
    • 0037459071 scopus 로고    scopus 로고
    • Functional sites in protein families uncovered via an objective and automated graph theoretic approach
    • A new prediction approach using graph theory that identifies recurring side-chain patterns in protein structures and includes an empirical calculation of statistical significance.
    • Wangikar P.P., Tendulkar A.V., Ramya S., Mail D.N., Sarawagi S. Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J Mol Biol. 326:2003;955-978 A new prediction approach using graph theory that identifies recurring side-chain patterns in protein structures and includes an empirical calculation of statistical significance.
    • (2003) J Mol Biol , vol.326 , pp. 955-978
    • Wangikar, P.P.1    Tendulkar, A.V.2    Ramya, S.3    Mail, D.N.4    Sarawagi, S.5
  • 10
    • 0037661398 scopus 로고    scopus 로고
    • A new bioinformatic approach to detect common 3D sites in protein structures
    • Jambon M., Imberty A., Deleage G., Geourjon C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins. 52:2003;137-145.
    • (2003) Proteins , vol.52 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Deleage, G.3    Geourjon, C.4
  • 11
    • 0037423759 scopus 로고    scopus 로고
    • An accurate, sensitive, and scalable method to identify functional sites in protein structures
    • An automated ET method that ranks the evolutionary importance of amino acids in protein sequences. This is the first method to quantify the significance of the overlap observed between the best ranked residues and functional sites.
    • Yao H., Kristensen D.M., Mihalek I., Sowa M.E., Shaw C., Kimmel M., Kavraki L., Lichtarge O. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol. 326:2003;255-261 An automated ET method that ranks the evolutionary importance of amino acids in protein sequences. This is the first method to quantify the significance of the overlap observed between the best ranked residues and functional sites.
    • (2003) J Mol Biol , vol.326 , pp. 255-261
    • Yao, H.1    Kristensen, D.M.2    Mihalek, I.3    Sowa, M.E.4    Shaw, C.5    Kimmel, M.6    Kavraki, L.7    Lichtarge, O.8
  • 12
    • 0019001660 scopus 로고
    • On the prediction of protein structure: The significance of root-mean-square deviation
    • Cohen F., Sternberg M. On the prediction of protein structure: the significance of root-mean-square deviation. J Mol Biol. 138:1980;321-333.
    • (1980) J Mol Biol , vol.138 , pp. 321-333
    • Cohen, F.1    Sternberg, M.2
  • 13
    • 0025275776 scopus 로고
    • Use of techniques derived from graph-theory to compare secondary structure motifs in proteins
    • Mitchell E.M., Artymiuk P.J., Rice D.W., Willett P. Use of techniques derived from graph-theory to compare secondary structure motifs in proteins. J Mol Biol. 212:1990;151-166.
    • (1990) J Mol Biol , vol.212 , pp. 151-166
    • Mitchell, E.M.1    Artymiuk, P.J.2    Rice, D.W.3    Willett, P.4
  • 14
    • 0027967593 scopus 로고
    • A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
    • Artymiuk P., Poirette A., Grindley H., Rice D., Willett P. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J Mol Biol. 243:1994;327-344.
    • (1994) J Mol Biol , vol.243 , pp. 327-344
    • Artymiuk, P.1    Poirette, A.2    Grindley, H.3    Rice, D.4    Willett, P.5
  • 16
    • 84976668743 scopus 로고
    • Algorithm 457-finding all cliques of an undirected graph
    • Bron C., Kerbosch J. Algorithm 457-finding all cliques of an undirected graph. Commun ACM. 16:1971;575-577.
    • (1971) Commun ACM , vol.16 , pp. 575-577
    • Bron, C.1    Kerbosch, J.2
  • 17
    • 0029913807 scopus 로고    scopus 로고
    • Evolutionary Trace method defines binding surfaces common to protein families
    • Lichtarge O., Bourne H., Cohen F. Evolutionary Trace method defines binding surfaces common to protein families. J Mol Biol. 257:1996;342-358.
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.2    Cohen, F.3
  • 18
    • 0031555477 scopus 로고    scopus 로고
    • Identification of functional surfaces of the zinc binding domains of intracellular receptors
    • Lichtarge O., Yamamoto K., Cohen F. Identification of functional surfaces of the zinc binding domains of intracellular receptors. J Mol Biol. 274:1997;325-337.
    • (1997) J Mol Biol , vol.274 , pp. 325-337
    • Lichtarge, O.1    Yamamoto, K.2    Cohen, F.3
  • 19
    • 0033613817 scopus 로고    scopus 로고
    • Evolutionary trace analysis of the Kunitz/BPTI family of proteins: Functional divergence may have been based on conformational adjustment
    • Pritchard L., Dufton M.J. Evolutionary trace analysis of the Kunitz/BPTI family of proteins: functional divergence may have been based on conformational adjustment. J Mol Biol. 285:1999;1589-1607.
    • (1999) J Mol Biol , vol.285 , pp. 1589-1607
    • Pritchard, L.1    Dufton, M.J.2
  • 20
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • Armon A., Graur D., Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol. 307:2001;447-463.
    • (2001) J Mol Biol , vol.307 , pp. 447-463
    • Armon, A.1    Graur, D.2    Ben-Tal, N.3
  • 21
    • 0034644783 scopus 로고    scopus 로고
    • Analysis and prediction of functional subtypes from protein sequence alignments
    • Hannenhalli S.S., Russell R.B. Analysis and prediction of functional subtypes from protein sequence alignments. J Mol Biol. 303:2000;61-76.
    • (2000) J Mol Biol , vol.303 , pp. 61-76
    • Hannenhalli, S.S.1    Russell, R.B.2
  • 22
    • 0036300444 scopus 로고    scopus 로고
    • Structural clusters of Evolutionary Tree residues are statistically significant and common in proteins
    • Madabushi S., Yao H., Marsh M., Kristensen D., Philippi A., Sowa M.E., Lichtarge O. Structural clusters of Evolutionary Tree residues are statistically significant and common in proteins. J Mol Biol. 316:2002;139-154.
    • (2002) J Mol Biol , vol.316 , pp. 139-154
    • Madabushi, S.1    Yao, H.2    Marsh, M.3    Kristensen, D.4    Philippi, A.5    Sowa, M.E.6    Lichtarge, O.7
  • 23
    • 0014689979 scopus 로고
    • Role of buried acid group in the mechanism of action of chymotrypsin
    • Blow D., Birktoft J., Hartley B. Role of buried acid group in the mechanism of action of chymotrypsin. Nature. 221:1969;337-340.
    • (1969) Nature , vol.221 , pp. 337-340
    • Blow, D.1    Birktoft, J.2    Hartley, B.3
  • 24
    • 0027967593 scopus 로고
    • A graph-theoretic approach to the identification of 3-dimensional patterns of amino-acid side-chains in protein structures
    • Artymiuk P.J., Poirrette A.R., Grindley H.M., Rice D.W., Willett P. A graph-theoretic approach to the identification of 3-dimensional patterns of amino-acid side-chains in protein structures. J Mol Biol. 243:1994;327-344.
    • (1994) J Mol Biol , vol.243 , pp. 327-344
    • Artymiuk, P.J.1    Poirrette, A.R.2    Grindley, H.M.3    Rice, D.W.4    Willett, P.5
  • 25
    • 0038128338 scopus 로고    scopus 로고
    • Searching for patterns of amino acids in 3D protein structures
    • Presents the background and an important update on the 10 year development of the ASSAM programme, which searches for patterns of amino acid side chains in protein structures using a pseudo-atom representation, and the Ullman sub-graph isomorphism algorithm.
    • Spriggs R.V., Artymiuk P.J., Willett P. Searching for patterns of amino acids in 3D protein structures. J Chem Inform Comp Sci. 43:2003;412-421 Presents the background and an important update on the 10 year development of the ASSAM programme, which searches for patterns of amino acid side chains in protein structures using a pseudo-atom representation, and the Ullman sub-graph isomorphism algorithm.
    • (2003) J Chem Inform Comp Sci , vol.43 , pp. 412-421
    • Spriggs, R.V.1    Artymiuk, P.J.2    Willett, P.3
  • 26
    • 0030724039 scopus 로고    scopus 로고
    • TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
    • Wallace A.C., Borkakoti N., Thornton J.M. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6:1997;2308-2323.
    • (1997) Protein Sci , vol.6 , pp. 2308-2323
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 27
    • 0029973830 scopus 로고    scopus 로고
    • Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
    • Wallace A.C., Laskowski R.A., Thornton J.M. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5:1996;1001-1013.
    • (1996) Protein Sci , vol.5 , pp. 1001-1013
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 28
    • 0141850386 scopus 로고    scopus 로고
    • An algorithm for constraint-based structural template matching: Application to 3D templates with statistical analysis
    • Presents JESS, an algorithm for searching protein structures for small groups of atoms that includes an empirical measure of significance. This algorithm is different in that it is designed as a flexible core around which to build constraint-based template search methods.
    • Barker J.A., Thornton J.M. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics. 19:2003;1644-1649 Presents JESS, an algorithm for searching protein structures for small groups of atoms that includes an empirical measure of significance. This algorithm is different in that it is designed as a flexible core around which to build constraint-based template search methods.
    • (2003) Bioinformatics , vol.19 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 29
    • 0042674397 scopus 로고    scopus 로고
    • Using a neural network and spatial clustering to predict the location of active sites in enzymes
    • Gutteridge A., Bartlett G.J., Thornton J.M. Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol. 330:2003;719-734.
    • (2003) J Mol Biol , vol.330 , pp. 719-734
    • Gutteridge, A.1    Bartlett, G.J.2    Thornton, J.M.3
  • 31
    • 0034868592 scopus 로고    scopus 로고
    • What is bioinformatics? a proposed definition and overview of the field
    • Luscombe N.M., Greenbaum D., Gerstein M. What is bioinformatics? A proposed definition and overview of the field. Methods Informat Med. 40:2001;346-358.
    • (2001) Methods Informat Med , vol.40 , pp. 346-358
    • Luscombe, N.M.1    Greenbaum, D.2    Gerstein, M.3
  • 33
    • 0037930733 scopus 로고    scopus 로고
    • Using structural motif templates to identify proteins with DNA binding function
    • Jones S., Barker J.A., Nobeli I., Thornton J.M. Using structural motif templates to identify proteins with DNA binding function. Nucl Acid Res. 31:2003;2811-2823.
    • (2003) Nucl Acid Res , vol.31 , pp. 2811-2823
    • Jones, S.1    Barker, J.A.2    Nobeli, I.3    Thornton, J.M.4
  • 34
    • 0038681269 scopus 로고    scopus 로고
    • Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif
    • McLaughlin W.A., Berman H.M. Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. J Mol Biol. 330:2003;43-55.
    • (2003) J Mol Biol , vol.330 , pp. 43-55
    • McLaughlin, W.A.1    Berman, H.M.2
  • 35
    • 0037470573 scopus 로고    scopus 로고
    • Annotating nucleic acid-binding function based on protein structure
    • Stawiski E.W., Gregoret L.M., Mandel-Gutfreund Y. Annotating nucleic acid-binding function based on protein structure. J Mol Biol. 326:2003;1065-1079.
    • (2003) J Mol Biol , vol.326 , pp. 1065-1079
    • Stawiski, E.W.1    Gregoret, L.M.2    Mandel-Gutfreund, Y.3
  • 38
    • 0042622410 scopus 로고    scopus 로고
    • WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures
    • Liang M.P., Banatao D.R., Klein T.E., Brutlag D.L., Altman R.B. WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucl Acid Res. 31:2003;3324-3327.
    • (2003) Nucl Acid Res , vol.31 , pp. 3324-3327
    • Liang, M.P.1    Banatao, D.R.2    Klein, T.E.3    Brutlag, D.L.4    Altman, R.B.5
  • 39
    • 0028950817 scopus 로고
    • Characterizing the microenvironment surrounding Pprotein sites
    • Bagley S.C., Altman R.B. Characterizing the microenvironment surrounding Pprotein sites. Prot Sci. 4:1995;622-635.
    • (1995) Prot Sci , vol.4 , pp. 622-635
    • Bagley, S.C.1    Altman, R.B.2
  • 40
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucl Acid Res. 31:2003;3370-3374.
    • (2003) Nucl Acid Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 41
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in non-homologous tertiary structures
    • Stark A., Russell R.B. Annotation in three dimensions. PINTS: patterns in non-homologous tertiary structures. Nucl Acids Res. 31:2003;3341-3344.
    • (2003) Nucl Acids Res , vol.31 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 42
    • 0038168191 scopus 로고    scopus 로고
    • Integrating structure, bioinformatics, and enzymology to discover function - BioH, a new carboxylesterase from Escherichia coli
    • One of the first papers to report on the assignment of function using a combination of theoretical and experimental techniques for a protein structure determined by a structural genomics consortium.
    • Sanishvili R., Yakunin A.F., Laskowski R.A., Skarina T., Evdokimova E., Doherty-Kirby A., Lajoie G.A., Thornton J.M., Arrowsmith C.H., Savchenko A. et al. Integrating structure, bioinformatics, and enzymology to discover function - BioH, a new carboxylesterase from Escherichia coli. J Biol Chem. 278:2003;26039-26045 One of the first papers to report on the assignment of function using a combination of theoretical and experimental techniques for a protein structure determined by a structural genomics consortium.
    • (2003) J Biol Chem , vol.278 , pp. 26039-26045
    • Sanishvili, R.1    Yakunin, A.F.2    Laskowski, R.A.3    Skarina, T.4    Evdokimova, E.5    Doherty-Kirby, A.6    Lajoie, G.A.7    Thornton, J.M.8    Arrowsmith, C.H.9    Savchenko, A.10


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