-
1
-
-
0242323639
-
Coverage of protein sequence space by current structural genomics targets
-
O'Toole N, Raymond S, Cygler M: Coverage of protein sequence space by current structural genomics targets. J Struct Funct Genomics 2003, 4(2-3):47-55.
-
(2003)
J Struct Funct Genomics
, vol.4
, Issue.2-3
, pp. 47-55
-
-
O'Toole, N.1
Raymond, S.2
Cygler, M.3
-
2
-
-
0031928367
-
Shining a light on structural genomics
-
Kim SH: Shining a light on structural genomics. Nat Struct Biol 1998, 5 Suppl:643-645.
-
(1998)
Nat Struct Biol
, vol.5
, Issue.SUPPL.
, pp. 643-645
-
-
Kim, S.H.1
-
3
-
-
0032521199
-
The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science
-
Shapiro L, Lima CD: The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. Structure 1998, 6(3):265-267.
-
(1998)
Structure
, vol.6
, Issue.3
, pp. 265-267
-
-
Shapiro, L.1
Lima, C.D.2
-
4
-
-
0032922524
-
The PRESAGE database for structural genomics
-
Brenner SE, Barken D, Levitt M: The PRESAGE database for structural genomics. Nucleic Acids Res 1999, 27(1):251-253.
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.1
, pp. 251-253
-
-
Brenner, S.E.1
Barken, D.2
Levitt, M.3
-
5
-
-
0034646354
-
Selecting protein targets for structural genomics of Pyrobaculum aerophilum: Validating automated fold assignment methods by using binary hypothesis testing
-
Mallick P, Goodwill KE, Fitz-Gibbon S, Miller JH, Eisenberg D: Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing. Proc Natl Acad Sci U S A 2000, 97(6):2450-2455.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, Issue.6
, pp. 2450-2455
-
-
Mallick, P.1
Goodwill, K.E.2
Fitz-Gibbon, S.3
Miller, J.H.4
Eisenberg, D.5
-
6
-
-
0033762813
-
Structural genomics projects in Japan
-
Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S: Structural genomics projects in Japan. Nat Struct Biol 2000, 7 Suppl:943-945.
-
(2000)
Nat Struct Biol
, vol.7
, Issue.SUPPL.
, pp. 943-945
-
-
Yokoyama, S.1
Hirota, H.2
Kigawa, T.3
Yabuki, T.4
Shirouzu, M.5
Terada, T.6
Ito, Y.7
Matsuo, Y.8
Kuroda, Y.9
Nishimura, Y.10
Kyogoku, Y.11
Miki, K.12
Masui, R.13
Kuramitsu, S.14
-
7
-
-
31144467558
-
The impact of structural genomics: Expectations and outcomes
-
Chandonia JM, Brenner SE: The impact of structural genomics: expectations and outcomes. Science 2006, 311(5759):347-351.
-
(2006)
Science
, vol.311
, Issue.5759
, pp. 347-351
-
-
Chandonia, J.M.1
Brenner, S.E.2
-
8
-
-
0344994534
-
NMR spectroscopy of large molecules and multimolecular assemblies in solution
-
Wider G, Wuthrich K: NMR spectroscopy of large molecules and multimolecular assemblies in solution. Curr Opin Struct Biol 1999, 9(5):594-601.
-
(1999)
Curr Opin Struct Biol
, vol.9
, Issue.5
, pp. 594-601
-
-
Wider, G.1
Wuthrich, K.2
-
9
-
-
0022429238
-
Folding of thermolysin fragments. Identification of the minimum size of a carboxyl-terminal fragment that can fold into a stable native-like structure
-
Dalzoppo D, Vita C, Fontana A: Folding of thermolysin fragments. Identification of the minimum size of a carboxyl-terminal fragment that can fold into a stable native-like structure. J Mol Biol 1985, 182(2):331-340.
-
(1985)
J Mol Biol
, vol.182
, Issue.2
, pp. 331-340
-
-
Dalzoppo, D.1
Vita, C.2
Fontana, A.3
-
10
-
-
0029873754
-
The domain organization of streptokinase: Nuclear magnetic resonance, circular dichroism, and functional characterization of proteolytic fragments
-
Parrado J, Conejero-Lara F, Smith RA, Marshall JM, Ponting CP, Dobson CM: The domain organization of streptokinase: nuclear magnetic resonance, circular dichroism, and functional characterization of proteolytic fragments. Protein Sci 1996, 5(4):693-704.
-
(1996)
Protein Sci
, vol.5
, Issue.4
, pp. 693-704
-
-
Parrado, J.1
Conejero-Lara, F.2
Smith, R.A.3
Marshall, J.M.4
Ponting, C.P.5
Dobson, C.M.6
-
11
-
-
0032539578
-
The structural aspects of limited proteolysis of native proteins
-
Hubbard SJ: The structural aspects of limited proteolysis of native proteins. Biochim Biophys Acta 1998, 1382(2):191-206.
-
(1998)
Biochim Biophys Acta
, vol.1382
, Issue.2
, pp. 191-206
-
-
Hubbard, S.J.1
-
12
-
-
33646093980
-
Identification of protein domains by shot-gun proteolysis
-
Epub 2006 Feb 13
-
Christ D, Winter G: Identification of protein domains by shot-gun proteolysis. J Mol Biol 2006, 358(2):364-71. Epub 2006 Feb 13.
-
(2006)
J Mol Biol
, vol.358
, Issue.2
, pp. 364-371
-
-
Christ, D.1
Winter, G.2
-
13
-
-
0033015460
-
Rapid protein-folding assay using green fluorescent protein
-
Waldo GS, Standish BM, Berendzen J, Terwilliger TC: Rapid protein-folding assay using green fluorescent protein. Nat Biotechnol 1999, 17(7):691-695.
-
(1999)
Nat Biotechnol
, vol.17
, Issue.7
, pp. 691-695
-
-
Waldo, G.S.1
Standish, B.M.2
Berendzen, J.3
Terwilliger, T.C.4
-
14
-
-
0037076312
-
Toward development of a screen to identify randomly encoded, foldable sequences
-
Epub 2002 May 7
-
Hagihara Y, Kim PS: Toward development of a screen to identify randomly encoded, foldable sequences. Proc Natl Acad Sci U S A 2002, 99(10):6619-24. Epub 2002 May 7.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, Issue.10
, pp. 6619-6624
-
-
Hagihara, Y.1
Kim, P.S.2
-
15
-
-
33645518215
-
Computer-aided NMR assay for detecting natively folded structural domains
-
Epub 2006 Mar 7
-
Hondoh T, Kato A, Yokoyama S, Kuroda Y: Computer-aided NMR assay for detecting natively folded structural domains. Protein Sci 2006, 15(4):871-83. Epub 2006 Mar 7.
-
(2006)
Protein Sci
, vol.15
, Issue.4
, pp. 871-883
-
-
Hondoh, T.1
Kato, A.2
Yokoyama, S.3
Kuroda, Y.4
-
16
-
-
0033957469
-
SMART: A web-based tool for the study of genetically mobile domains
-
Schultz J, Copley RR, Doerks T, Ponting CP, Bork P: SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res 2000, 28(1):231-234.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 231-234
-
-
Schultz, J.1
Copley, R.R.2
Doerks, T.3
Ponting, C.P.4
Bork, P.5
-
17
-
-
0032568655
-
SMART, a simple modular architecture research tool: Identification of signaling domains
-
Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 1998, 95(11):5857-5864.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, Issue.11
, pp. 5857-5864
-
-
Schultz, J.1
Milpetz, F.2
Bork, P.3
Ponting, C.P.4
-
18
-
-
0011542799
-
The Pfam protein families database
-
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30(1):276-280.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.1
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
19
-
-
0036087630
-
CDD: A database of conserved domain alignments with links to domain three-dimensional structure
-
Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH: CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 2002, 30(1):281-283.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.1
, pp. 281-283
-
-
Marchler-Bauer, A.1
Panchenko, A.R.2
Shoemaker, B.A.3
Thiessen, P.A.4
Geer, L.Y.5
Bryant, S.H.6
-
20
-
-
0034493084
-
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics
-
Kuroda Y, Tani K, Matsuo Y, Yokoyama S: Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. Protein Sci 2000, 9(12):2313-2321.
-
(2000)
Protein Sci
, vol.9
, Issue.12
, pp. 2313-2321
-
-
Kuroda, Y.1
Tani, K.2
Matsuo, Y.3
Yokoyama, S.4
-
21
-
-
0036721254
-
Protein domain identification and improved sequence similarity searching using PSI-BLAST
-
George RA, Heringa J: Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins 2002, 48(4):672-681.
-
(2002)
Proteins
, vol.48
, Issue.4
, pp. 672-681
-
-
George, R.A.1
Heringa, J.2
-
22
-
-
16644363065
-
Delineation of modular proteins: Domain boundary prediction from sequence information
-
Kong L, Ranganathan S: Delineation of modular proteins: domain boundary prediction from sequence information. Brief Bioinform 2004, 5(2):179-192.
-
(2004)
Brief Bioinform
, vol.5
, Issue.2
, pp. 179-192
-
-
Kong, L.1
Ranganathan, S.2
-
23
-
-
0024057934
-
Prediction of the location of structural domains in globular proteins
-
Kikuchi T, Nemethy G, Scheraga HA: Prediction of the location of structural domains in globular proteins. J Protein Chem 1988, 7(4):427-471.
-
(1988)
J Protein Chem
, vol.7
, Issue.4
, pp. 427-471
-
-
Kikuchi, T.1
Nemethy, G.2
Scheraga, H.A.3
-
24
-
-
0033753811
-
Domain size distributions can predict domain boundaries
-
Wheelan SJ, Marchler-Bauer A, Bryant SH: Domain size distributions can predict domain boundaries. Bioinformatics 2000, 16(7):613-618.
-
(2000)
Bioinformatics
, vol.16
, Issue.7
, pp. 613-618
-
-
Wheelan, S.J.1
Marchler-Bauer, A.2
Bryant, S.H.3
-
25
-
-
0036288851
-
Characterization and prediction of linker sequences of multi-domain proteins by a neural network
-
Miyazaki S, Kuroda Y, Yokoyama S: Characterization and prediction of linker sequences of multi-domain proteins by a neural network. J Struct Funct Genomics 2002, 2(1):37-51.
-
(2002)
J Struct Funct Genomics
, vol.2
, Issue.1
, pp. 37-51
-
-
Miyazaki, S.1
Kuroda, Y.2
Yokoyama, S.3
-
26
-
-
17844363963
-
PPRODO: Prediction of protein domain boundaries using neural networks
-
Sim J, Kim SY, Lee J: PPRODO: prediction of protein domain boundaries using neural networks. Proteins 2005, 59(3):627-632.
-
(2005)
Proteins
, vol.59
, Issue.3
, pp. 627-632
-
-
Sim, J.1
Kim, S.Y.2
Lee, J.3
-
27
-
-
3042810008
-
Sequence-based prediction of protein domains
-
Liu J, Rost B: Sequence-based prediction of protein domains. Nucleic Acids Res 2004, 32(12):3522-3530.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.12
, pp. 3522-3530
-
-
Liu, J.1
Rost, B.2
-
28
-
-
33645741221
-
Improvement of domain linker prediction by incorporating loop-length-dependent characteristics
-
Tanaka T, Yokoyama S, Kuroda Y: Improvement of domain linker prediction by incorporating loop-length-dependent characteristics. Biopolymers 2006, 84(2):161-168.
-
(2006)
Biopolymers
, vol.84
, Issue.2
, pp. 161-168
-
-
Tanaka, T.1
Yokoyama, S.2
Kuroda, Y.3
-
29
-
-
0242292025
-
Characteristics and prediction of domain linker sequences in multi-domain proteins
-
Tanaka T, Kuroda Y, Yokoyama S: Characteristics and prediction of domain linker sequences in multi-domain proteins. J Struct Funct Genomics 2003, 4(2-3):79-85.
-
(2003)
J Struct Funct Genomics
, vol.4
, Issue.2-3
, pp. 79-85
-
-
Tanaka, T.1
Kuroda, Y.2
Yokoyama, S.3
-
30
-
-
21744461895
-
Armadillo: Domain boundary prediction by amino acid composition
-
Dumontier M, Yao R, Feldman HJ, Hogue CW: Armadillo: domain boundary prediction by amino acid composition. J Mol Biol 2005, 350(5):1061-1073.
-
(2005)
J Mol Biol
, vol.350
, Issue.5
, pp. 1061-1073
-
-
Dumontier, M.1
Yao, R.2
Feldman, H.J.3
Hogue, C.W.4
-
31
-
-
0036220048
-
Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments
-
Rigden DJ: Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. Protein Eng 2002, 15(2):65-77.
-
(2002)
Protein Eng
, vol.15
, Issue.2
, pp. 65-77
-
-
Rigden, D.J.1
-
32
-
-
0036306348
-
SnapDRAGON: A method to delineate protein structural domains from sequence data
-
George RA, Heringa J: SnapDRAGON: a method to delineate protein structural domains from sequence data. J Mol Biol 2002, 316(3):839-851.
-
(2002)
J Mol Biol
, vol.316
, Issue.3
, pp. 839-851
-
-
George, R.A.1
Heringa, J.2
-
33
-
-
0026672260
-
Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks
-
Hirst JD, Sternberg MJ: Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochemistry 1992, 31(32):7211-7218.
-
(1992)
Biochemistry
, vol.31
, Issue.32
, pp. 7211-7218
-
-
Hirst, J.D.1
Sternberg, M.J.2
-
34
-
-
0023803244
-
Predicting the secondary structure of globular proteins using neural network models
-
Qian N, Sejnowski TJ: Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 1988, 202(4):865-884.
-
(1988)
J Mol Biol
, vol.202
, Issue.4
, pp. 865-884
-
-
Qian, N.1
Sejnowski, T.J.2
-
35
-
-
0027291015
-
Prediction of protein secondary structure at better than 70% accuracy
-
Rost B, Sander C: Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993, 232(2):584-599.
-
(1993)
J Mol Biol
, vol.232
, Issue.2
, pp. 584-599
-
-
Rost, B.1
Sander, C.2
-
36
-
-
0032900496
-
Prediction of the location and type of beta-turns in proteins using neural networks
-
Shepherd AJ, Gorse D, Thornton JM: Prediction of the location and type of beta-turns in proteins using neural networks. Protein Sci 1999, 8(5):1045-1055.
-
(1999)
Protein Sci
, vol.8
, Issue.5
, pp. 1045-1055
-
-
Shepherd, A.J.1
Gorse, D.2
Thornton, J.M.3
-
37
-
-
0028906598
-
Neural networks for secondary structure and structural class predictions
-
Chandonia JM, Karplus M: Neural networks for secondary structure and structural class predictions. Protein Sci 1995, 4(2):275-285.
-
(1995)
Protein Sci
, vol.4
, Issue.2
, pp. 275-285
-
-
Chandonia, J.M.1
Karplus, M.2
-
38
-
-
0031551577
-
Stabilization centers in proteins: Identification, characterization and predictions
-
Dosztanyi Z, Fiser A, Simon I: Stabilization centers in proteins: identification, characterization and predictions. J Mol Biol 1997, 272(4):597-612.
-
(1997)
J Mol Biol
, vol.272
, Issue.4
, pp. 597-612
-
-
Dosztanyi, Z.1
Fiser, A.2
Simon, I.3
-
39
-
-
0033957834
-
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
-
Bairoch A, Apweiler R: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000, 28(1):45-48.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 45-48
-
-
Bairoch, A.1
Apweiler, R.2
-
40
-
-
0036084625
-
SCOP database in 2002: Refinements accommodate structural genomics
-
Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG: SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002, 30(1):264-267.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.1
, pp. 264-267
-
-
Lo Conte, L.1
Brenner, S.E.2
Hubbard, T.J.3
Chothia, C.4
Murzin, A.G.5
-
41
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28(1):235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
42
-
-
0029901640
-
Analysis of compositionally biased regions in sequence databases
-
Wootton JC, Federhen S: Analysis of compositionally biased regions in sequence databases. Methods Enzymol 1996, 266:554-571.
-
(1996)
Methods Enzymol
, vol.266
, pp. 554-571
-
-
Wootton, J.C.1
Federhen, S.2
-
43
-
-
0035188314
-
Sequence complexity of disordered protein
-
Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK: Sequence complexity of disordered protein. Proteins 2001, 42(1):38-48.
-
(2001)
Proteins
, vol.42
, Issue.1
, pp. 38-48
-
-
Romero, P.1
Obradovic, Z.2
Li, X.3
Garner, E.C.4
Brown, C.J.5
Dunker, A.K.6
-
44
-
-
0015914842
-
Logical analysis of the mechanism of protein folding. I. Predictions of helices, loops and beta-structures from primary structure
-
Nagano K: Logical analysis of the mechanism of protein folding. I. Predictions of helices, loops and beta-structures from primary structure. J Mol Biol 1973, 75(2):401-420.
-
(1973)
J Mol Biol
, vol.75
, Issue.2
, pp. 401-420
-
-
Nagano, K.1
-
45
-
-
0015079203
-
Predictions of structural homologies in cytochrome c proteins
-
Lewis PN, Scheraga HA: Predictions of structural homologies in cytochrome c proteins. Arch Biochem Biophys 1971, 144(2):576-583.
-
(1971)
Arch Biochem Biophys
, vol.144
, Issue.2
, pp. 576-583
-
-
Lewis, P.N.1
Scheraga, H.A.2
-
46
-
-
0015987426
-
Prediction of protein conformation
-
Chou PY, Fasman GD: Prediction of protein conformation. Biochemistry 1974, 13(2):222-245.
-
(1974)
Biochemistry
, vol.13
, Issue.2
, pp. 222-245
-
-
Chou, P.Y.1
Fasman, G.D.2
-
47
-
-
0037248878
-
The Protein Data Bank and structural genomics
-
Westbrook J, Feng Z, Chen L, Yang H, Berman HM: The Protein Data Bank and structural genomics. Nucleic Acids Res 2003, 31(1):489-491.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 489-491
-
-
Westbrook, J.1
Feng, Z.2
Chen, L.3
Yang, H.4
Berman, H.M.5
-
48
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
49
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
50
-
-
0022471098
-
Learning representations by back-propagating errors
-
R.J.W:
-
Rumelhart DE, Hinton GE, R.J. W: Learning representations by back-propagating errors. Nature 1986, 323:533-536.
-
(1986)
Nature
, vol.323
, pp. 533-536
-
-
Rumelhart, D.E.1
Hinton, G.E.2
-
51
-
-
0028501914
-
Non-globular domains in protein sequences: Automated segmentation using complexity measures
-
Wootton JC: Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 1994, 18(3):269-285.
-
(1994)
Comput Chem
, vol.18
, Issue.3
, pp. 269-285
-
-
Wootton, J.C.1
|