-
1
-
-
0033757822
-
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
-
2
-
-
0037248878
-
The Protein Data Bank and structural genomics
-
Westbrook J., Feng Z.K., Chen L., Yang H.W., Berman H.M. The Protein Data Bank and structural genomics. Nucl Acid Res. 31:2003;489-491.
-
(2003)
Nucl Acid Res
, vol.31
, pp. 489-491
-
-
Westbrook, J.1
Feng, Z.K.2
Chen, L.3
Yang, H.W.4
Berman, H.M.5
-
3
-
-
0034753838
-
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
-
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
-
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
-
6
-
-
0033757840
-
From structure to function: Approaches and limitations
-
Thornton J.M., Todd A.E., Milburn D., Borkakoti N., Orengo C.A. From structure to function: approaches and limitations. Nat Struc Biol. 7:2000;991-994.
-
(2000)
Nat Struc Biol
, vol.7
, pp. 991-994
-
-
Thornton, J.M.1
Todd, A.E.2
Milburn, D.3
Borkakoti, N.4
Orengo, C.A.5
-
7
-
-
0032527783
-
Protein folds and functions
-
Martin A.C., Orengo C.A., Hutchinson E.G., Jones S., Karmirantzou M., Laskowski R.A., Mitchell J.B., Taroni C., Thornton J.M. Protein folds and functions. Structure. 6:1998;875-884.
-
(1998)
Structure
, vol.6
, pp. 875-884
-
-
Martin, A.C.1
Orengo, C.A.2
Hutchinson, E.G.3
Jones, S.4
Karmirantzou, M.5
Laskowski, R.A.6
Mitchell, J.B.7
Taroni, C.8
Thornton, J.M.9
-
8
-
-
0037424601
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
15
-
-
0026951618
-
Similarity searching in databases of 3-dimensional molecules and macromolecules
-
Artymiuk P.J., Bath P.A., Grindley H.M., Pepperrell C.A., Poirrette A.R., Rice D.W., Thorner D.A., Wild D.J., Willett P., Allen F.H., Taylor R. Similarity searching in databases of 3-dimensional molecules and macromolecules. J Chem Info Computer Sci. 32:1992;617-630.
-
(1992)
J Chem Info Computer Sci
, vol.32
, pp. 617-630
-
-
Artymiuk, P.J.1
Bath, P.A.2
Grindley, H.M.3
Pepperrell, C.A.4
Poirrette, A.R.5
Rice, D.W.6
Thorner, D.A.7
Wild, D.J.8
Willett, P.9
Allen, F.H.10
Taylor, R.11
-
16
-
-
84976668743
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
32
-
-
0026742978
-
The nucleic-acid database - A comprehensive relational database of 3-dimensional structures of nucleic-acids
-
Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.H., Srinivasan A.R., Schneider B. The nucleic-acid database - a comprehensive relational database of 3-dimensional structures of nucleic-acids. Biophys J. 63:1992;751-759.
-
(1992)
Biophys J
, vol.63
, pp. 751-759
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, J.4
Gelbin, A.5
Demeny, T.6
Hsieh, S.H.7
Srinivasan, A.R.8
Schneider, B.9
-
33
-
-
0037930733
-
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
-
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
-
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
-
37
-
-
0036616218
-
The Protein Data Bank
-
Berman H.M., Battistuz T., Bhat T.N., Bluhm W.F., Bourne P.E., Burkhardt K., Iype L., Jain S., Fagan P., Marvin J. et al. The Protein Data Bank. Acta Cryst D. 58:2002;899-907.
-
(2002)
Acta Cryst D
, vol.58
, pp. 899-907
-
-
Berman, H.M.1
Battistuz, T.2
Bhat, T.N.3
Bluhm, W.F.4
Bourne, P.E.5
Burkhardt, K.6
Iype, L.7
Jain, S.8
Fagan, P.9
Marvin, J.10
-
38
-
-
0042622410
-
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
-
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
-
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
-
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
-
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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