-
1
-
-
0027174134
-
Prediction of protein secondary structure by the hidden Markov model
-
Asai, K., Hayamizu, S., and Handa, K.I. 1993. Prediction of protein secondary structure by the hidden Markov model. Comp. Applic. Biosci. 9(2), 141-146.
-
(1993)
Comp. Applic. Biosci.
, vol.9
, Issue.2
, pp. 141-146
-
-
Asai, K.1
Hayamizu, S.2
Handa, K.I.3
-
2
-
-
0024541195
-
Algorithms for the optimal identification of segment neighborhoods
-
Auger, I.E., and Lawrence, C.E. 1989. Algorithms for the optimal identification of segment neighborhoods. Bull. Math. Biol. 51(1), 39-54.
-
(1989)
Bull. Math. Biol.
, vol.51
, Issue.1
, pp. 39-54
-
-
Auger, I.E.1
Lawrence, C.E.2
-
4
-
-
0029149907
-
Protein secondary structure prediction
-
Barton, G.J. 1995. Protein secondary structure prediction. Curr. Opin. Struct. Biol. 5, 372-376.
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 372-376
-
-
Barton, G.J.1
-
5
-
-
0029188711
-
Predicting the conformation of proteins from sequences: Progress and future progress
-
Benner, S.A. 1995. Predicting the conformation of proteins from sequences: progress and future progress. J. Mol. Recogn. 8, 9-28.
-
(1995)
J. Mol. Recogn.
, vol.8
, pp. 9-28
-
-
Benner, S.A.1
-
6
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macro-molecular structures
-
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. 1977. The Protein Data Bank: a computer-based archival file for macro-molecular structures. J. Mol. Biol. 112, 535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
7
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
Burge, C., and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
8
-
-
0015987426
-
Prediction of protein conformation
-
Chou, P.Y., and Fasman, U.D. 1974. Prediction of protein conformation. Biochemistry 13, 211-215.
-
(1974)
Biochemistry
, vol.13
, pp. 211-215
-
-
Chou, P.Y.1
Fasman, U.D.2
-
9
-
-
0023048287
-
Turn prediction in proteins using a pattern-matching approach
-
Cohen, F.E., Abarbanel, R.M., Kuntz, I.D., and Fletterick, R.J. 1986. Turn prediction in proteins using a pattern-matching approach. Biochemistry 25, 266-275.
-
(1986)
Biochemistry
, vol.25
, pp. 266-275
-
-
Cohen, F.E.1
Abarbanel, R.M.2
Kuntz, I.D.3
Fletterick, R.J.4
-
10
-
-
0027207221
-
Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment
-
Colloc'h, N., Etchebest, C., Thoreau, E., Henrissat, B., and Mornon, J.-P. 1993. Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng. 6(4), 377-382.
-
(1993)
Protein Eng.
, vol.6
, Issue.4
, pp. 377-382
-
-
Colloc'h, N.1
Etchebest, C.2
Thoreau, E.3
Henrissat, B.4
Mornon, J.-P.5
-
11
-
-
0030054216
-
Improving protein secondary structure prediction with aligned homologous sequences
-
Di Francesco, V., Gamier, J., and Munson, P.J. 1996. Improving protein secondary structure prediction with aligned homologous sequences. Protein Science 5, 106-113.
-
(1996)
Protein Science
, vol.5
, pp. 106-113
-
-
Di Francesco, V.1
Gamier, J.2
Munson, P.J.3
-
12
-
-
0029020484
-
N- and C-capping preferences for all 20 amino acids in α-helical peptides
-
Doig, A.J., and Baldwin, R.L. 1995. N- and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Science 4, 1325-1336.
-
(1995)
Protein Science
, vol.4
, pp. 1325-1336
-
-
Doig, A.J.1
Baldwin, R.L.2
-
13
-
-
0028289435
-
Determination of free energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N- and C-capping
-
Doig, A.J., Chakrabartty, A., Klingler, T.M., and Baldwin, R.L. 1994. Determination of free energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N- and C-capping. Biochemistry 33, 3396-3403.
-
(1994)
Biochemistry
, vol.33
, pp. 3396-3403
-
-
Doig, A.J.1
Chakrabartty, A.2
Klingler, T.M.3
Baldwin, R.L.4
-
15
-
-
0000929505
-
The hydrophobic moment detects periodicity in protein hydrophobicity
-
Eisenberg, D., Weiss, R.M., and Terwilliger, T.C. 1984. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. USA 81, 140-144.
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 140-144
-
-
Eisenberg, D.1
Weiss, R.M.2
Terwilliger, T.C.3
-
16
-
-
0029874551
-
Protein fold recognition using sequence-derived predictions
-
Fischer, D., and Eisenberg, D. 1996. Protein fold recognition using sequence-derived predictions. Protein Science 5, 947-955.
-
(1996)
Protein Science
, vol.5
, pp. 947-955
-
-
Fischer, D.1
Eisenberg, D.2
-
18
-
-
0029996162
-
Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence
-
Frishman, D., and Argos, P 1996. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng. 9(2), 133-142.
-
(1996)
Protein Eng.
, vol.9
, Issue.2
, pp. 133-142
-
-
Frishman, D.1
Argos, P.2
-
19
-
-
0030931336
-
Seventy-five percent accuracy in protein secondary structure prediction
-
Frishman, D., and Argos, P 1997. Seventy-five percent accuracy in protein secondary structure prediction. Proteins: Struct. Funct. Genet. 27, 329-335.
-
(1997)
Proteins: Struct. Funct. Genet.
, vol.27
, pp. 329-335
-
-
Frishman, D.1
Argos, P.2
-
20
-
-
0029884694
-
GOR method for predicting protein secondary structure from amino acid sequence
-
Garnier, J., Gibrat, J.-F., and Robson, B. 1996. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 266, 540-553.
-
(1996)
Methods Enzymol
, vol.266
, pp. 540-553
-
-
Garnier, J.1
Gibrat, J.-F.2
Robson, B.3
-
21
-
-
0017873321
-
Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
-
Garnier, J., Osguthorpe, D.J., and Robson, B. 1978. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120, 97-120.
-
(1978)
J. Mol. Biol.
, vol.120
, pp. 97-120
-
-
Garnier, J.1
Osguthorpe, D.J.2
Robson, B.3
-
22
-
-
0027102226
-
OBSTRUCT: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity
-
Heringa, J., Sommerfeldt, H., Higgins, D., and Argos, P. 1992. OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. CABIOS 8(6), 599-600.
-
(1992)
CABIOS
, vol.8
, Issue.6
, pp. 599-600
-
-
Heringa, J.1
Sommerfeldt, H.2
Higgins, D.3
Argos, P.4
-
23
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm, U., and Sander, C. 1994. Enlarged representative set of protein structures. Protein Science 3, 522-524.
-
(1994)
Protein Science
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
24
-
-
0000268209
-
Protein secondary structure prediction with a neural network
-
Holley, H.L., and Karplus, M. 1989. Protein secondary structure prediction with a neural network. Proc. Natl. Acad. Sci. USA 86, 152-156.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 152-156
-
-
Holley, H.L.1
Karplus, M.2
-
25
-
-
0028211273
-
A model recognition approach to the prediction of all-helical membrane protein structure and topology
-
Jones, D.T., Taylor, W.R., and Thornton, J.M. 1994. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33, 3038-3049.
-
(1994)
Biochemistry
, vol.33
, pp. 3038-3049
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
26
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W., and Sander, C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
27
-
-
0027960477
-
Discovering structural correlations in α-helices
-
Klingler, T.M., and Brutlag, D.L. 1994. Discovering structural correlations in α-helices. Protein Science 3, 1847-1857.
-
(1994)
Protein Science
, vol.3
, pp. 1847-1857
-
-
Klingler, T.M.1
Brutlag, D.L.2
-
28
-
-
0028181441
-
Hidden Markov models in computational biology: Applications to protein modeling
-
Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. 1994. Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol. 235, 1501-1531.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
29
-
-
0028303384
-
A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions
-
Krylov, D., Mikhailenko, I., and Vinson, C. 1994. A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions. EMBO Journal 13(12), 2849-2861.
-
(1994)
EMBO Journal
, vol.13
, Issue.12
, pp. 2849-2861
-
-
Krylov, D.1
Mikhailenko, I.2
Vinson, C.3
-
30
-
-
0030333286
-
A generalized hidden Markov model for the recognition of human genes in DNA
-
Kulp, D., Haussler, D., Reese, M.G., and Eeckman, F.H. 1996. A generalized hidden Markov model for the recognition of human genes in DNA. Fourth Intntl. Conf. Intell. Sys. Mol. Biol.
-
(1996)
Fourth Intntl. Conf. Intell. Sys. Mol. Biol.
-
-
Kulp, D.1
Haussler, D.2
Reese, M.G.3
Eeckman, F.H.4
-
31
-
-
0027912333
-
Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
-
Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F., and Wootton, J.C. 1993. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
32
-
-
0022685753
-
Continuously variable duration hidden Markov models for automatic speech recognition
-
Levinson, S.E. 1986. Continuously variable duration hidden Markov models for automatic speech recognition. Computer Speech and Language 1, 29-45.
-
(1986)
Computer Speech and Language
, vol.1
, pp. 29-45
-
-
Levinson, S.E.1
-
33
-
-
0019317336
-
Specific recognition in the tertiary structure of β-sheets of proteins
-
Lifson, S., and Sander, C. 1980. Specific recognition in the tertiary structure of β-sheets of proteins. J. Mol. Biol. 139, 627-639.
-
(1980)
J. Mol. Biol.
, vol.139
, pp. 627-639
-
-
Lifson, S.1
Sander, C.2
-
35
-
-
0442325057
-
Markovian structures in biological sequence alignments
-
Liu, J.S., Neuwald, A., and Lawrence, C.E. 1999. Markovian structures in biological sequence alignments. J. Amer. Statist. Assoc. 94, 1-15.
-
(1999)
J. Amer. Statist. Assoc.
, vol.94
, pp. 1-15
-
-
Liu, J.S.1
Neuwald, A.2
Lawrence, C.E.3
-
36
-
-
84950424966
-
Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
-
Liu, J.S., Neuwald, A.F., and Lawrence, C.E. 1995. Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J. Amer. Statist. Assoc. 90, 1156-1170.
-
(1995)
J. Amer. Statist. Assoc.
, vol.90
, pp. 1156-1170
-
-
Liu, J.S.1
Neuwald, A.F.2
Lawrence, C.E.3
-
37
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews, B.W. 1975. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405, 442-451.
-
(1975)
Biochim. Biophys. Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
38
-
-
0028283339
-
An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure
-
Monge, A., Friesner, R.A., and Honig, B. 1994. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc. Natl. Acad. Sci. USA 91, 5027-5029.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 5027-5029
-
-
Monge, A.1
Friesner, R.A.2
Honig, B.3
-
40
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.Z., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.Z.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
42
-
-
0026596926
-
A segment-based approach to protein secondary structure prediction
-
Presnell, S.R., Cohen, B.I., and Cohen, F.E. 1992. A segment-based approach to protein secondary structure prediction. Biochemistry 31, 983-993.
-
(1992)
Biochemistry
, vol.31
, pp. 983-993
-
-
Presnell, S.R.1
Cohen, B.I.2
Cohen, F.E.3
-
43
-
-
0024290488
-
Helix signal in proteins
-
Presta, L.G., and Rose, G.D. 1988. Helix signal in proteins. Science 240, 1632-1641.
-
(1988)
Science
, vol.240
, pp. 1632-1641
-
-
Presta, L.G.1
Rose, G.D.2
-
44
-
-
0023803244
-
Predicting the secondary structure of globular proteins using neural network models
-
Qian, N., and Sejnowski, T.J. 1988. Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 202, 865-884.
-
(1988)
J. Mol. Biol.
, vol.202
, pp. 865-884
-
-
Qian, N.1
Sejnowski, T.J.2
-
45
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner, L.R. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77(2), 257-286.
-
(1989)
Proc. IEEE
, vol.77
, Issue.2
, pp. 257-286
-
-
Rabiner, L.R.1
-
46
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of α-helices
-
Richardson and Richardson. 1988. Amino acid preferences for specific locations at the ends of α-helices. Science 240, 1648-1652.
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson1
Richardson2
-
47
-
-
0029984070
-
Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments
-
Riis, S.K., and Krogh, A. 1996. Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments. J. Comp. Biol. 3(1), 163-183.
-
(1996)
J. Comp. Biol.
, vol.3
, Issue.1
, pp. 163-183
-
-
Riis, S.K.1
Krogh, A.2
-
48
-
-
0030038634
-
Topology prediction for helical transmembrane proteins at 86% accuracy
-
Rost, B., Fariselli, P., and Casadio, R. 1996. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Science 5, 1704-1718.
-
(1996)
Protein Science
, vol.5
, pp. 1704-1718
-
-
Rost, B.1
Fariselli, P.2
Casadio, R.3
-
49
-
-
0027169638
-
Improved prediction of protein secondary structure by use of sequence profiles and neural networks
-
Rost, B., and Sander, C. 1993a. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl. Acad. Sci. USA 90, 7558-7562.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 7558-7562
-
-
Rost, B.1
Sander, C.2
-
50
-
-
0027291015
-
Prediction of protein secondary structure at better than 70% accuracy
-
Rost, B., and Sander, C. 1993b. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232, 584-599.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 584-599
-
-
Rost, B.1
Sander, C.2
-
51
-
-
0028300741
-
Combining evolutionary information and neural networks to predict protein secondary structure
-
Rost, B., and Sander, C. 1994. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins Struct. Funct. Genet. 19, 55-72.
-
(1994)
Proteins Struct. Funct. Genet.
, vol.19
, pp. 55-72
-
-
Rost, B.1
Sander, C.2
-
52
-
-
0003202794
-
Pedestrian guide to analysing sequence databases
-
Ashman, K., ed. Springer, Heidelberg
-
Rost, B., and Schneider, R. 1997. Pedestrian guide to analysing sequence databases. In Core techniques in biochemistry Ashman, K., ed. Springer, Heidelberg.
-
(1997)
Core Techniques in Biochemistry
-
-
Rost, B.1
Schneider, R.2
-
53
-
-
0022234383
-
Explicit modelling of state occupancy in hidden Markov models for automatic speech recognition
-
Russell, M.J., and Moore, R.K. 1985. Explicit modelling of state occupancy in hidden Markov models for automatic speech recognition. ICASSP, Tampa, FL.
-
(1985)
ICASSP, Tampa, FL
-
-
Russell, M.J.1
Moore, R.K.2
-
54
-
-
0029951995
-
Protein fold recognition by mapping predicted secondary structures
-
Russell, R.B., Copley, R.R., and Barton, G.J. 1996. Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259, 349-365.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 349-365
-
-
Russell, R.B.1
Copley, R.R.2
Barton, G.J.3
-
55
-
-
0028965118
-
Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments
-
Salamov, A.A., and Solovyev, V.V. 1995. Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J. Mol. Biol. 247, 11-15.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 11-15
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
56
-
-
0031585987
-
Protein secondary structure prediction using local alignments
-
Salamov, A.A., and Solovyev, V.V. 1997. Protein secondary structure prediction using local alignments. J. Mol. Biol. 268, 31-36.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 31-36
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
59
-
-
0028792105
-
Guidelines for protein design: The energetics of β-sheet side chain interactions
-
Smith, C.K., and Regan, L. 1995. Guidelines for protein design: the energetics of β-sheet side chain interactions. Science 270, 980-982.
-
(1995)
Science
, vol.270
, pp. 980-982
-
-
Smith, C.K.1
Regan, L.2
-
60
-
-
0028605560
-
Predicting α-helix and β-strand segments of globular proteins
-
Solovyev, V.V., and Salamov, A.A. 1994. Predicting α-helix and β-strand segments of globular proteins. Comput. Appl. Biosci. 10(6), 661-669.
-
(1994)
Comput. Appl. Biosci.
, vol.10
, Issue.6
, pp. 661-669
-
-
Solovyev, V.V.1
Salamov, A.A.2
-
61
-
-
0028822255
-
Addition of side chain interactions to modified Lifson-Roig helix-coil theory: Application to energetics of phenylalanine-methionine interactions
-
Stapley, B.J., Rohl, C.A., and Doig, A.J. 1995. Addition of side chain interactions to modified Lifson-Roig helix-coil theory: Application to energetics of phenylalanine-methionine interactions. Protein Science 4, 2383-2391.
-
(1995)
Protein Science
, vol.4
, pp. 2383-2391
-
-
Stapley, B.J.1
Rohl, C.A.2
Doig, A.J.3
-
62
-
-
0026682530
-
Predicting protein secondary structure using neural net and statistical methods
-
Stolorz, P., Lapedes, A., and Xia, Y. 1992. Predicting protein secondary structure using neural net and statistical methods. J. Mol. Biol. 225, 363-377.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 363-377
-
-
Stolorz, P.1
Lapedes, A.2
Xia, Y.3
-
63
-
-
0027477526
-
Structural analysis based on state-space modeling
-
Stultz, C.M., White, J.V., and Smith, T.F. 1993. Structural analysis based on state-space modeling. Protein Science 2, 305-314.
-
(1993)
Protein Science
, vol.2
, pp. 305-314
-
-
Stultz, C.M.1
White, J.V.2
Smith, T.F.3
-
65
-
-
0027199670
-
Protein secondary structure prediction using nearest-neighbor methods
-
Yi, T.-M., and Lander, E.S. 1993. Protein secondary structure prediction using nearest-neighbor methods. J. Mol. Biol. 232, 1117-1129.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 1117-1129
-
-
Yi, T.-M.1
Lander, E.S.2
-
66
-
-
0026771388
-
Hybrid system for protein secondary structure prediction
-
Zhang, X., Mesirov, J.P., and Waltz, D.L. 1992. Hybrid system for protein secondary structure prediction. J. Mol. Biol. 225, 1049-1063.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 1049-1063
-
-
Zhang, X.1
Mesirov, J.P.2
Waltz, D.L.3
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