-
1
-
-
0034697986
-
What can disulfide bonds tell us about protein energetics, function and folding: Simulations and bioinformatics analysis
-
V.I. Abkevich, and E.I. Shakhnovich What can disulfide bonds tell us about protein energetics, function and folding simulations and bioinformatics analysis J. Mol. Biol. 300 2000 975 985
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 975-985
-
-
Abkevich, V.I.1
Shakhnovich, E.I.2
-
2
-
-
0015859467
-
Principles that govern the folding of protein chains
-
C.B. Anfinsen Principles that govern the folding of protein chains Science 181 1973 223 230
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
3
-
-
0033954256
-
The Protein Data Bank
-
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242
-
(2000)
Nucleic Acids Res.
, vol.28
, 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
-
4
-
-
0027362677
-
Disulfide bonds and the stability of globular proteins
-
S.F. Betz Disulfide bonds and the stability of globular proteins Protein Sci 2 1993 1551 1558
-
(1993)
Protein Sci
, vol.2
, pp. 1551-1558
-
-
Betz, S.F.1
-
5
-
-
0034602774
-
Knowledge-based analysis of microarray gene expression data by using support vector machines
-
M.P.S. Brown, W.N. Grundy, D. Lin, N. Cristianini, C.W. Sugnet, T.S. Furey, M. Ares, and D. Haussler Knowledge-based analysis of microarray gene expression data by using support vector machines Proc. Natl Acad. Sci. 97 2000 262 267
-
(2000)
Proc. Natl Acad. Sci.
, vol.97
, pp. 262-267
-
-
Brown, M.P.S.1
Grundy, W.N.2
Lin, D.3
Cristianini, N.4
Sugnet, C.W.5
Furey, T.S.6
Ares, M.7
Haussler, D.8
-
6
-
-
0002100813
-
-
Burbidge, R., Trotter, M., Holden, S., Buxton, B., 2000. Proceedings of the AISB'00 Symposium on Artificial Intelligence in Bioinformatics, pp. 1-4.
-
(2000)
Proceedings of the AISB'00 Symposium on Artificial Intelligence in Bioinformatics
, pp. 1-4
-
-
Burbidge, R.1
Trotter, M.2
Holden, S.3
Buxton, B.4
-
7
-
-
0034436969
-
Support vector machines for prediction of protein subcellular location
-
Y.D. Cai, X.J. Liu, X.B. Xu, and K.C. Chou Support vector machines for prediction of protein subcellular location Mol. Cell Biol. Res. Commun. 4 2000 230 233
-
(2000)
Mol. Cell Biol. Res. Commun.
, vol.4
, pp. 230-233
-
-
Cai, Y.D.1
Liu, X.J.2
Xu, X.B.3
Chou, K.C.4
-
8
-
-
0036007085
-
Prediction of protein structural classes by support vector machines
-
Y.D. Cai, X.J. Liu, X.B. Xu, and K.C. Chou Prediction of protein structural classes by support vector machines Comput. Chem. 26 2002 293 296
-
(2002)
Comput. Chem.
, vol.26
, pp. 293-296
-
-
Cai, Y.D.1
Liu, X.J.2
Xu, X.B.3
Chou, K.C.4
-
9
-
-
0037423777
-
Support vector machines for prediction of protein subcellular location
-
Y.D. Cai, X.J. Liu, X.B. Xu, and K.C. Chou Support vector machines for prediction of protein subcellular location J. Theor. Biol. 221 2003 115 120
-
(2003)
J. Theor. Biol.
, vol.221
, pp. 115-120
-
-
Cai, Y.D.1
Liu, X.J.2
Xu, X.B.3
Chou, K.C.4
-
11
-
-
0141990705
-
Predicting the disulfide bonding state of cysteines with combinations of kernel machines
-
A. Ceroni, P. Frasconi, A. Passerini, and A. Vullo Predicting the disulfide bonding state of cysteines with combinations of kernel machines J. VLSI Signal Process. 35 2003 287 295
-
(2003)
J. VLSI Signal Process.
, vol.35
, pp. 287-295
-
-
Ceroni, A.1
Frasconi, P.2
Passerini, A.3
Vullo, A.4
-
12
-
-
0037195776
-
Using functional domain composition and support vector machines for prediction of protein subcellular location
-
K.C. Chou, and Y.D. Cai Using functional domain composition and support vector machines for prediction of protein subcellular location J. Biol. Chem. 277 2002 45765 45769
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 45765-45769
-
-
Chou, K.C.1
Cai, Y.D.2
-
13
-
-
0041819762
-
Relationship between protein structures and disulfide-bonding patterns
-
C.C. Chuang, C.Y. Chen, J.M. Yang, P.C. Lyu, and J.K. Hwang Relationship between protein structures and disulfide-bonding patterns Proteins 53 2004 1 5
-
(2004)
Proteins
, vol.53
, pp. 1-5
-
-
Chuang, C.C.1
Chen, C.Y.2
Yang, J.M.3
Lyu, P.C.4
Hwang, J.K.5
-
14
-
-
0034491013
-
The effects of disulfide bonds on the denatured state of barnase
-
J. Clarke, A.M. Hounslow, C.J. Bond, A.R. Fersht, and V. Daggett The effects of disulfide bonds on the denatured state of barnase Protein Sci. 9 2000 2394 2404
-
(2000)
Protein Sci.
, vol.9
, pp. 2394-2404
-
-
Clarke, J.1
Hounslow, A.M.2
Bond, C.J.3
Fersht, A.R.4
Daggett, V.5
-
16
-
-
0029653850
-
Disulfide-coupled protein folding pathways
-
T. Creighton Disulfide-coupled protein folding pathways Philos. Trans. R. Soc. London B 348 1995 5 10
-
(1995)
Philos. Trans. R. Soc. London B
, vol.348
, pp. 5-10
-
-
Creighton, T.1
-
17
-
-
0026692715
-
Protein engineering of a disulfide bond in a beta/alpha-barrel protein
-
J. Eder, and M. Wilmanns Protein engineering of a disulfide bond in a beta/alpha-barrel protein Biochemistry 31 1992 4437 4444
-
(1992)
Biochemistry
, vol.31
, pp. 4437-4444
-
-
Eder, J.1
Wilmanns, M.2
-
18
-
-
0034781580
-
Prediction of disulfide connectivity in proteins
-
P. Fariselli, and R. Casadio Prediction of disulfide connectivity in proteins Bioinformatics 17 2001 957 964
-
(2001)
Bioinformatics
, vol.17
, pp. 957-964
-
-
Fariselli, P.1
Casadio, R.2
-
19
-
-
0033566578
-
Role of evolutionary information in predicting the disulfide bonding state of cysteine in proteins
-
P. Fariselli, P. Riccobelli, and R. Casadio Role of evolutionary information in predicting the disulfide bonding state of cysteine in proteins Proteins 36 1999 340 346
-
(1999)
Proteins
, vol.36
, pp. 340-346
-
-
Fariselli, P.1
Riccobelli, P.2
Casadio, R.3
-
20
-
-
1842492440
-
A neural network-based method for predicting the disulfide connectivity in proteins
-
Damiani, E. et al. (Eds.), IOS Press
-
Fariselli, P., Martelli, P.L., Casadio, R., 2002. A neural network-based method for predicting the disulfide connectivity in proteins. In: Damiani, E. et al. (Eds.), Knowledge Based Intelligent Information Engineering Systems and Allied Technologies (KES 2002), vol. 1, IOS Press, pp. 464-468.
-
(2002)
Knowledge Based Intelligent Information Engineering Systems and Allied Technologies (KES 2002)
, vol.1
, pp. 464-468
-
-
Fariselli, P.1
Martelli, P.L.2
Casadio, R.3
-
21
-
-
0034039497
-
Predicting the oxidation state of cysteines by multiple sequence alignment
-
A. Fiser, and I. Simon Predicting the oxidation state of cysteines by multiple sequence alignment Bioinformatics 16 2000 251 256
-
(2000)
Bioinformatics
, vol.16
, pp. 251-256
-
-
Fiser, A.1
Simon, I.2
-
22
-
-
0026579140
-
Different sequence environment of cysteines and half cystines in proteins: Application to predict disulfide forming residues
-
A. Fiser, M. Cserzo, E. Tudos, and I. Simon Different sequence environment of cysteines and half cystines in proteins application to predict disulfide forming residues FEBS Lett. 302 1992 117 120
-
(1992)
FEBS Lett.
, vol.302
, pp. 117-120
-
-
Fiser, A.1
Cserzo, M.2
Tudos, E.3
Simon, I.4
-
24
-
-
0028063090
-
Analysis and classification of disulphide connectivity in proteins: The entropic effect of cross-linkage
-
P.M. Harrison, and M.J.E. Sternberg Analysis and classification of disulphide connectivity in proteins the entropic effect of cross-linkage J. Mol. Biol. 244 1994 448 463
-
(1994)
J. Mol. Biol.
, vol.244
, pp. 448-463
-
-
Harrison, P.M.1
Sternberg, M.J.E.2
-
25
-
-
0035957531
-
A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach
-
S.J. Hua, and Z.R. Sun A novel method of protein secondary structure prediction with high segment overlap measure support vector machine approach J. Mol. Biol. 308 2001 397 407
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 397-407
-
-
Hua, S.J.1
Sun, Z.R.2
-
26
-
-
0034843744
-
Support vector machine approach for protein subcellular localization prediction
-
S.J. Hua, and Z.R. Sun Support vector machine approach for protein subcellular localization prediction Bioinformatics 17 2001 721 728
-
(2001)
Bioinformatics
, vol.17
, pp. 721-728
-
-
Hua, S.J.1
Sun, Z.R.2
-
27
-
-
0033516514
-
Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions
-
E.S. Huang, R. Samudrala, and J.W. Ponder Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions J. Mol. Biol. 290 1999 267 281
-
(1999)
J. Mol. Biol.
, vol.290
, pp. 267-281
-
-
Huang, E.S.1
Samudrala, R.2
Ponder, J.W.3
-
28
-
-
0347093598
-
Prediction of protein subcellular locations using fuzzy k-NN method
-
Y. Huang, and Y.D. Li Prediction of protein subcellular locations using fuzzy k-NN method Bioinformatics 20 2004 21 28
-
(2004)
Bioinformatics
, vol.20
, pp. 21-28
-
-
Huang, Y.1
Li, Y.D.2
-
31
-
-
0141593924
-
Protein secondary prediction based on an improved support vector machines approach
-
H. Kim, and H. Park Protein secondary prediction based on an improved support vector machines approach Protein Eng. 16 2003 553 560
-
(2003)
Protein Eng.
, vol.16
, pp. 553-560
-
-
Kim, H.1
Park, H.2
-
32
-
-
0028138294
-
The adsorption protein of filamentous phage fd: Assignment of its disulphide bridges and identification of the domain incorporated in the coat
-
A. Kremser, and I. Rasched The adsorption protein of filamentous phage fd assignment of its disulphide bridges and identification of the domain incorporated in the coat Biochemistry 33 1994 13954 13958
-
(1994)
Biochemistry
, vol.33
, pp. 13954-13958
-
-
Kremser, A.1
Rasched, I.2
-
33
-
-
0003607151
-
-
Academic Press, London
-
Mardia, K.V., Kent, J.T., Bibby, J.M., 1979. Multivariate Analysis. Academic Press, London, pp. 322, 381.
-
(1979)
Multivariate Analysis
, pp. 322
-
-
Mardia, K.V.1
Kent, J.T.2
Bibby, J.M.3
-
34
-
-
0036937367
-
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks
-
P.L. Martelli, P. Fariselli, L. Malaguti, and R. Casadio Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks Protein Eng. 15 2002 951 953
-
(2002)
Protein Eng.
, vol.15
, pp. 951-953
-
-
Martelli, P.L.1
Fariselli, P.2
Malaguti, L.3
Casadio, R.4
-
35
-
-
0036839271
-
Prediction of the disulfide bonding state of cysteines in proteins at 88% accuracy
-
P.L. Martelli, P. Fariselli, L. Malaguti, and R. Casadio Prediction of the disulfide bonding state of cysteines in proteins at 88% accuracy Protein Sci. 11 2002 2735 2739
-
(2002)
Protein Sci.
, vol.11
, pp. 2735-2739
-
-
Martelli, P.L.1
Fariselli, P.2
Malaguti, L.3
Casadio, R.4
-
36
-
-
0024564552
-
Control of enzyme activity by an engineered disulfide bond
-
M. Matsumura, and B. Matthews Control of enzyme activity by an engineered disulfide bond Science 243 1989 792 794
-
(1989)
Science
, vol.243
, pp. 792-794
-
-
Matsumura, M.1
Matthews, B.2
-
37
-
-
0026319603
-
Stabilization of functional proteins by introduction of multiple disulfide bonds
-
M. Matsumura, and B. Matthews Stabilization of functional proteins by introduction of multiple disulfide bonds Method Enzymot. 202 1991 336 355
-
(1991)
Method Enzymot.
, vol.202
, pp. 336-355
-
-
Matsumura, M.1
Matthews, B.2
-
38
-
-
0016772212
-
Comparison of predicted and observed secondary structure of T4 phage lysozyme
-
B.W. Matthews Comparison of predicted and observed secondary structure of T4 phage lysozyme Biophys. Acta 405 1975 442 451
-
(1975)
Biophys. Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
39
-
-
0022425563
-
A new method for rapid assignment of s-s bridges in proteins
-
H. Morris, and P. Pucci A new method for rapid assignment of s-s bridges in proteins Biochem. Biophys. Res. Commun. 126 1985 1122 1128
-
(1985)
Biochem. Biophys. Res. Commun.
, vol.126
, pp. 1122-1128
-
-
Morris, H.1
Pucci, P.2
-
40
-
-
0037083493
-
Predicting the disulfide bonding state of cysteines using protein descriptors
-
M.H. Mucchielli-Giorgi, S. Hazout, and P. Tuffery Predicting the disulfide bonding state of cysteines using protein descriptors Proteins 46 2002 243 249
-
(2002)
Proteins
, vol.46
, pp. 243-249
-
-
Mucchielli-Giorgi, M.H.1
Hazout, S.2
Tuffery, P.3
-
41
-
-
0025118064
-
Prediction of the disulfide-bonding state of cysteine in proteins
-
S.M. Muskal, S.R. Holbrook, and S.H. Kim Prediction of the disulfide-bonding state of cysteine in proteins Protein Eng. 3 1990 667 672
-
(1990)
Protein Eng.
, vol.3
, pp. 667-672
-
-
Muskal, S.M.1
Holbrook, S.R.2
Kim, S.H.3
-
42
-
-
0030777303
-
CATH - A hierarchic classification of protein domain structures
-
C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton CATH - a hierarchic classification of protein domain structures Structure 8 1997 1093 1108
-
(1997)
Structure
, vol.8
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
43
-
-
0033985050
-
Assigning genomic sequences to CATH
-
F.M.G. Pearl, D. Lee, J.E. Bray, I. Sillitoe, A.E. Todd, A.P. Harrison, J.M. Thornton, and C.A. Orengo Assigning genomic sequences to CATH Nucleic Acids Res. 1 2000 277 282
-
(2000)
Nucleic Acids Res.
, vol.1
, pp. 277-282
-
-
Pearl, F.M.G.1
Lee, D.2
Bray, J.E.3
Sillitoe, I.4
Todd, A.E.5
Harrison, A.P.6
Thornton, J.M.7
Orengo, C.A.8
-
44
-
-
0032788590
-
Amino acid neighbours and detailed conformational analysis of cysteines in proteins
-
M.T. Petersen, P.H. Jonson, and S.B. Petersen Amino acid neighbours and detailed conformational analysis of cysteines in proteins Protein Eng. 12 1999 535 548
-
(1999)
Protein Eng.
, vol.12
, pp. 535-548
-
-
Petersen, M.T.1
Jonson, P.H.2
Petersen, S.B.3
-
45
-
-
0031575423
-
MONSSTER: A method for folding globular proteins with a small number of distance restraints
-
J. Skolnick, A. Kolinski, and A.R. Ortiz MONSSTER a method for folding globular proteins with a small number of distance restraints J. Mol. Biol. 265 1997 217 241
-
(1997)
J. Mol. Biol.
, vol.265
, pp. 217-241
-
-
Skolnick, J.1
Kolinski, A.2
Ortiz, A.R.3
-
48
-
-
0346493041
-
A novel database of disulfide patterns and its application to the discovery of distantly related homologs
-
H.W. Van Vlijmen, A. Gupta, L.S. Narasimhan, and J. Singh A novel database of disulfide patterns and its application to the discovery of distantly related homologs J. Mol. Biol. 335 2004 1083 1092
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 1083-1092
-
-
Van Vlijmen, H.W.1
Gupta, A.2
Narasimhan, L.S.3
Singh, J.4
-
49
-
-
1842455284
-
Disulfide connectivity prediction using recursive neural networks and evolutionary information
-
A. Vullo, and P. Frasconi Disulfide connectivity prediction using recursive neural networks and evolutionary information Bioinformatics 20 2004 653 659
-
(2004)
Bioinformatics
, vol.20
, pp. 653-659
-
-
Vullo, A.1
Frasconi, P.2
-
50
-
-
0043180474
-
PISCES: A protein sequence culling server
-
G. Wang, and R.L. Dunbrack Jr. PISCES a protein sequence culling server Bioinformatics 19 2003 1589 1591
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
51
-
-
0842265197
-
Support vector machines for prediction of peptidyl prolyl cis/trans isomerization
-
M.L. Wang, W.J. Li, and W.B. Xu Support vector machines for prediction of peptidyl prolyl cis/trans isomerization J. Peptide Res. 63 2003 23 28
-
(2003)
J. Peptide Res.
, vol.63
, pp. 23-28
-
-
Wang, M.L.1
Li, W.J.2
Xu, W.B.3
-
52
-
-
0040786272
-
-
W.J. Wedemeyer, E. Welkler, M. Narayan, and H.A. Scheraga Disulfide bonds and protein folding, Biochemistry 39 2000 4207 4216
-
(2000)
Disulfide Bonds and Protein Folding, Biochemistry
, vol.39
, pp. 4207-4216
-
-
Wedemeyer, W.J.1
Welkler, E.2
Narayan, M.3
Scheraga, H.A.4
-
54
-
-
0028943316
-
Disulfide bond formation and eukaryotic secretory productivity
-
K.D. Wittrup Disulfide bond formation and eukaryotic secretory productivity Curr. Opin. in Biotechnol. 6 1995 203 208
-
(1995)
Curr. Opin. in Biotechnol.
, vol.6
, pp. 203-208
-
-
Wittrup, K.D.1
-
55
-
-
0027998241
-
Determination of the disulfide bridges in factor va heavy rain
-
J. Xue, M. Kalafatis, J.R. Silveira, C. Kung, and K.G. Mann Determination of the disulfide bridges in factor va heavy rain Biochemistry 33 1994 13019 13116
-
(1994)
Biochemistry
, vol.33
, pp. 13019-13116
-
-
Xue, J.1
Kalafatis, M.2
Silveira, J.R.3
Kung, C.4
Mann, K.G.5
-
56
-
-
0035819416
-
A new approach to predict the helix/strand content of globular Proteins
-
Z. Zhang, Z.R. Sun, and C.T. Zhang A new approach to predict the helix/strand content of globular Proteins J. Theor. Biol. 208 2001 65 78
-
(2001)
J. Theor. Biol.
, vol.208
, pp. 65-78
-
-
Zhang, Z.1
Sun, Z.R.2
Zhang, C.T.3
-
57
-
-
0027480940
-
Disulfide bond contribution to protein stability: Positional effects of substitution in the hydrophobic core of the two-stranded alpha-helical coiled-coil
-
N.E. Zhou, C.M. Kay, and R.S. Hodges Disulfide bond contribution to protein stability positional effects of substitution in the hydrophobic core of the two-stranded alpha-helical coiled-coil Biochemistry 32 1993 178 187
-
(1993)
Biochemistry
, vol.32
, pp. 178-187
-
-
Zhou, N.E.1
Kay, C.M.2
Hodges, R.S.3
|