-
1
-
-
0030049315
-
Review: Prediction of HIV protease cleavage sites in proteins
-
Chou KC. Review: Prediction of HIV protease cleavage sites in proteins. Anal Biochem 1996;233(1):1-14.
-
(1996)
Anal Biochem
, vol.233
, Issue.1
, pp. 1-14
-
-
Chou, K.C.1
-
2
-
-
0023046815
-
A new method for predicting signal sequence cleavage sites
-
Von Heijne G. A new method for predicting signal sequence cleavage sites. Nucleic Acids Res 1986;14(11):4683.
-
(1986)
Nucleic Acids Res
, vol.14
, Issue.11
, pp. 4683
-
-
Von Heijne, G.1
-
3
-
-
0029595415
-
Neural network prediction of the HIV-1 protease cleavage sites
-
Thompson TB, Chou KC, Zheng C. Neural network prediction of the HIV-1 protease cleavage sites. J. Theoretical Biol 1995;177(4):369-79.
-
(1995)
J. Theoretical Biol
, vol.177
, Issue.4
, pp. 369-379
-
-
Thompson, T.B.1
Chou, K.C.2
Zheng, C.3
-
4
-
-
0032017815
-
Artificial neural network model for predicting HIV protease cleavage sites in protein
-
Cai YD, Chou KC. Artificial neural network model for predicting HIV protease cleavage sites in protein. Adv in Eng Softw 1998;29(2):119-128.
-
(1998)
Adv in Eng Softw
, vol.29
, Issue.2
, pp. 119-128
-
-
Cai, Y.D.1
Chou, K.C.2
-
5
-
-
0037258751
-
Support vector machines for prediction of protein signal sequences and their cleavage sites
-
Cai YD, Lin S, Chou KC. Support vector machines for prediction of protein signal sequences and their cleavage sites. Peptides 2003;24(1):159-61.
-
(2003)
Peptides
, vol.24
, Issue.1
, pp. 159-161
-
-
Cai, Y.D.1
Lin, S.2
Chou, K.C.3
-
6
-
-
4444262024
-
Why neural networks should not be used for HIV-1 protease cleavage site prediction
-
Rögnvaldsson T, You L. Why neural networks should not be used for HIV-1 protease cleavage site prediction. Bioinformatics 2004;20(11):1702-109.
-
(2004)
Bioinformatics
, vol.20
, Issue.11
, pp. 1702-2109
-
-
Rögnvaldsson, T.1
You, L.2
-
7
-
-
40649104302
-
Hivcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins
-
Shen HB, Chou KC. Hivcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins. Analytical Biochemistry 2008;375(2):388-90.
-
(2008)
Analytical Biochemistry
, vol.375
, Issue.2
, pp. 388-390
-
-
Shen, H.B.1
Chou, K.C.2
-
8
-
-
23144444029
-
Grabcas: a bioinformatics tool for score-based prediction of caspase-and granzyme B-cleavage sites in protein sequences
-
Backes C, Kuentzer J, Lenhof HP, et al. Grabcas: a bioinformatics tool for score-based prediction of caspase-and granzyme B-cleavage sites in protein sequences. NucleicAcidsRes 2005;33(Suppl. 2):W208.
-
(2005)
NucleicAcidsRes
, vol.33
, Issue.SUPPL. 2
-
-
Backes, C.1
Kuentzer, J.2
Lenhof, H.P.3
-
9
-
-
84871967410
-
Svm-based prediction of caspase substrate cleavage sites
-
Wee L, Tan T, Ranganathan S. Svm-based prediction of caspase substrate cleavage sites. BMC Bioinformatics 2006; 7(Suppl 5):S14.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL 5
-
-
Wee, L.1
Tan, T.2
Ranganathan, S.3
-
10
-
-
18744369642
-
Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks
-
Yang ZR. Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks. Bioinformatics 2005;21(9):1831.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1831
-
-
Yang, Z.R.1
-
11
-
-
79955780941
-
Calpain cleavage prediction using multiple kernel learning
-
duVerle D, Ono Y, Sorimachi H, et al. Calpain cleavage prediction using multiple kernel learning. PLoS One 2011; 6(5):e19035.
-
(2011)
PLoS One
, vol.6
, Issue.5
-
-
duVerle, D.1
Ono, Y.2
Sorimachi, H.3
-
12
-
-
0032479445
-
Functional defects of a muscle-specific calpain, p94, caused by mutations associated with limb-girdle muscular dystrophy type 2A
-
Ono Y, Shimada H, Sorimachi H, et al. Functional defects of a muscle-specific calpain, p94, caused by mutations associated with limb-girdle muscular dystrophy type 2A. J Biol Chem 1998;273(27):17073.
-
(1998)
J Biol Chem
, vol.273
, Issue.27
, pp. 17073
-
-
Ono, Y.1
Shimada, H.2
Sorimachi, H.3
-
13
-
-
0028905205
-
Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A
-
Richard I, Broux O, Allamand V, et al. Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A. Cell 1995;81(1):27-40.
-
(1995)
Cell
, vol.81
, Issue.1
, pp. 27-40
-
-
Richard, I.1
Broux, O.2
Allamand, V.3
-
14
-
-
34447650074
-
Calpains and their multiple roles in diabetes mellitus
-
Harris F, Biswas S, Singh J, et al. Calpains and their multiple roles in diabetes mellitus. Ann NYAcad Sci 2006; 1084:452.
-
(2006)
Ann NYAcad Sci
, vol.1084
, pp. 452
-
-
Harris, F.1
Biswas, S.2
Singh, J.3
-
15
-
-
0033772073
-
Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus
-
Horikawa Y, Oda N, Cox NJ, et al. Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet 2000;26(2):163-75.
-
(2000)
Nat Genet
, vol.26
, Issue.2
, pp. 163-175
-
-
Horikawa, Y.1
Oda, N.2
Cox, N.J.3
-
16
-
-
0034426280
-
Calpain-dependent proteolysis of NF2 protein: involvement in schwannomas and meningiomas
-
Kimura Y, Saya H, Nakao M. Calpain-dependent proteolysis of NF2 protein: involvement in schwannomas and meningiomas. Neuropathology 2000;20(3):153-60.
-
(2000)
Neuropathology
, vol.20
, Issue.3
, pp. 153-160
-
-
Kimura, Y.1
Saya, H.2
Nakao, M.3
-
19
-
-
0021827776
-
Redesigning trypsin: alteration of substrate specificity
-
Craik CS, Largman C, Fletcher T, etal. Redesigning trypsin: alteration of substrate specificity. Science 1985;228(4697): 291.
-
(1985)
Science
, vol.228
, Issue.4697
, pp. 291
-
-
Craik, C.S.1
Largman, C.2
Fletcher, T.3
-
20
-
-
70449378957
-
Caspase substrates: easily caught in deep waters?
-
Demon D, Van Damme P, Berghe TV, et al. Caspase substrates: easily caught in deep waters? Trends Biotechnol 2009; 27:680-88.
-
(2009)
Trends Biotechnol
, vol.27
, pp. 680-688
-
-
Demon, D.1
Van Damme, P.2
Berghe, T.V.3
-
21
-
-
33744961634
-
Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities
-
Choe Y, Leonetti F, Greenbaum DC, et al. Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities. J Biol Chem 2006;281(18):12824.
-
(2006)
J Biol Chem
, vol.281
, Issue.18
, pp. 12824
-
-
Choe, Y.1
Leonetti, F.2
Greenbaum, D.C.3
-
24
-
-
77954637447
-
CaMPDB: a resource for calpain and modulatory proteolysis
-
duVerle D, Takigawa I, Ono Y, et al. CaMPDB: a resource for calpain and modulatory proteolysis. Genome Inform 2010. 22:202.
-
(2010)
Genome Inform
, vol.22
, pp. 202
-
-
duVerle, D.1
Takigawa, I.2
Ono, Y.3
-
25
-
-
0023323994
-
A unique specificity of a calcium activated neutral protease indicated in histone hydrolysis
-
Sakai K, Akanuma H, Imahori K, et al. A unique specificity of a calcium activated neutral protease indicated in histone hydrolysis. J Biochem 1987;101(4):911.
-
(1987)
J Biochem
, vol.101
, Issue.4
, pp. 911
-
-
Sakai, K.1
Akanuma, H.2
Imahori, K.3
-
26
-
-
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):865-84.
-
(1988)
J Mol Biol
, vol.202
, Issue.4
, pp. 865-884
-
-
Qian, N.1
Sejnowski, T.J.2
-
27
-
-
1842455240
-
Bio-support vector machines for computational proteomics
-
Yang ZR, Chou KC. Bio-support vector machines for computational proteomics. Bioinformatics 2004;20(5):735.
-
(2004)
Bioinformatics
, vol.20
, Issue.5
, pp. 735
-
-
Yang, Z.R.1
Chou, K.C.2
-
28
-
-
22944452794
-
Applying support vector machines to imbalanced datasets
-
Akbani R, Kwek S, Japkowicz N. Applying support vector machines to imbalanced datasets. Machine Learning: ECML 2004 2004;39-50.
-
(2004)
Machine Learning: ECML
, vol.2004
, pp. 39-50
-
-
Akbani, R.1
Kwek, S.2
Japkowicz, N.3
-
29
-
-
0003562954
-
A simple generalisation of the area under the roc curve for multiple class classification problems
-
Hand DJ, Till RJ. A simple generalisation of the area under the roc curve for multiple class classification problems. Machine Learning 2001;45(2):171-86.
-
(2001)
Machine Learning
, vol.45
, Issue.2
, pp. 171-186
-
-
Hand, D.J.1
Till, R.J.2
-
30
-
-
0025008168
-
Sequence logos: a new way to display consensus sequences
-
Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990; 18(20):6097.
-
(1990)
Nucleic Acids Res
, vol.18
, Issue.20
, pp. 6097
-
-
Schneider, T.D.1
Stephens, R.M.2
-
31
-
-
0026345896
-
A cumulative specificity model for proteases from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base
-
Poorman RA, Tomasselli AG, Heinrikson RL, et al. A cumulative specificity model for proteases from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base. JBiolChem 1991; 266(22):14554.
-
(1991)
JBiolChem
, vol.266
, Issue.22
, pp. 14554
-
-
Poorman, R.A.1
Tomasselli, A.G.2
Heinrikson, R.L.3
-
32
-
-
0028043552
-
Position-based sequence weights
-
Henikoff S, Henikoff JG. Position-based sequence weights. JMol Biol 1994;243(4):574-78.
-
(1994)
JMol Biol
, vol.243
, Issue.4
, pp. 574-578
-
-
Henikoff, S.1
Henikoff, J.G.2
-
34
-
-
0022631926
-
The folding type of a protein is relevant to the amino acid composition
-
Nakashima H, Nishikawa K, Ooi T. The folding type of a protein is relevant to the amino acid composition. JBiochem 1986;99(1):153.
-
(1986)
JBiochem
, vol.99
, Issue.1
, pp. 153
-
-
Nakashima, H.1
Nishikawa, K.2
Ooi, T.3
-
35
-
-
0029977162
-
Using substitution probabilities to improve position-specific scoring matrices
-
Henikoff JG, Henikoff S. Using substitution probabilities to improve position-specific scoring matrices. Comp Appl Biosci: CABIOS 1996;12(2):135.
-
(1996)
Comp Appl Biosci: CABIOS
, vol.12
, Issue.2
, pp. 135
-
-
Henikoff, J.G.1
Henikoff, S.2
-
36
-
-
0028800739
-
A vector projection method for predicting the specificity of GalNAc-transferase
-
Chou KC, Zhang CT, Kézdy FJ, et al. A vector projection method for predicting the specificity of GalNAc-transferase. Proteins: Struct Funct Bioinf 1995;21(2):118-26.
-
(1995)
Proteins: Struct Funct Bioinf
, vol.21
, Issue.2
, pp. 118-126
-
-
Chou, K.C.1
Zhang, C.T.2
Kézdy, F.J.3
-
37
-
-
0034946412
-
Determination of protease cleavage site motifs using mixture-based oriented peptide libraries
-
Turk BE, Huang LL, Piro ET, et al. Determination of protease cleavage site motifs using mixture-based oriented peptide libraries. Nature Biotechnol 2001;19(7):661-67.
-
(2001)
Nature Biotechnol
, vol.19
, Issue.7
, pp. 661-667
-
-
Turk, B.E.1
Huang, L.L.2
Piro, E.T.3
-
38
-
-
27144505097
-
Protein identification and analysis tools on the expasy server
-
Totowa, NJ: Humana Press
-
Gasteiger E, Hoogland C, Gattiker A, et al. Protein identification and analysis tools on the expasy server. Proteomics Protocols Handbook. Totowa, NJ: Humana Press, 2005;571-607.
-
(2005)
Proteomics Protocols Handbook
, pp. 571-607
-
-
Gasteiger, E.1
Hoogland, C.2
Gattiker, A.3
-
39
-
-
29144473665
-
Caspredictor: a new computer-based tool for caspase substrate prediction
-
Garay-Malpartida HM, Occhiucci JM, Alves J, et al. Caspredictor: a new computer-based tool for caspase substrate prediction. Bioinformatics 2005;21(Suppl. 1):i169.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Garay-Malpartida, H.M.1
Occhiucci, J.M.2
Alves, J.3
-
40
-
-
0141506120
-
Characterizing proteolytic cleavage site activity using bio-basis function neural networks
-
Thomson R, Hodgman TC, Yang ZR, et al. Characterizing proteolytic cleavage site activity using bio-basis function neural networks. Bioinformatics 2003;19(14):1741.
-
(2003)
Bioinformatics
, vol.19
, Issue.14
, pp. 1741
-
-
Thomson, R.1
Hodgman, T.C.2
Yang, Z.R.3
-
42
-
-
13844272392
-
Bio-basis function neural network for prediction of protease cleavage sites in proteins
-
Yang ZR, Thomson R. Bio-basis function neural network for prediction of protease cleavage sites in proteins. Neural Networks, IEEETrans 2005;16(1):263-74.
-
(2005)
Neural Networks, IEEETrans
, vol.16
, Issue.1
, pp. 263-274
-
-
Yang, Z.R.1
Thomson, R.2
-
43
-
-
0024861871
-
Approximation by superpositions of a sigmoidal function
-
Cybenko G. Approximation by superpositions of a sigmoidal function. MCSS 1989;2(4):303-14.
-
(1989)
MCSS
, vol.2
, Issue.4
, pp. 303-314
-
-
Cybenko, G.1
-
44
-
-
0001447184
-
Neural network studies. comparison of overfitting and overtraining
-
Tetko IV, Livingstone DJ, Luik AI. Neural network studies. comparison of overfitting and overtraining. JChemInform Comp Sci 1995;35(5):826-33.
-
(1995)
JChemInform Comp Sci
, vol.35
, Issue.5
, pp. 826-833
-
-
Tetko, I.V.1
Livingstone, D.J.2
Luik, A.I.3
-
45
-
-
0038824700
-
Toward computer-based cleavage site prediction of cysteine endopeptidases
-
Lohmüller T, Wenzler D, Hagemann S, et al. Toward computer-based cleavage site prediction of cysteine endopeptidases. Biol Chem 2003;384(6):899.
-
(2003)
Biol Chem
, vol.384
, Issue.6
, pp. 899
-
-
Lohmüller, T.1
Wenzler, D.2
Hagemann, S.3
-
46
-
-
2442718801
-
On the sequential determinants of calpain cleavage
-
Tompa P, Buzder-Lantos P, Tantos A, et al. On the sequential determinants of calpain cleavage. J Biol Chem 2004; 279(20):20775.
-
(2004)
J Biol Chem
, vol.279
, Issue.20
, pp. 20775
-
-
Tompa, P.1
Buzder-Lantos, P.2
Tantos, A.3
-
47
-
-
77954272392
-
Pripper: prediction of caspase cleavage sites from whole proteomes
-
Piippo M, Lietzen N, Nevalainen OS, et al. Pripper: prediction of caspase cleavage sites from whole proteomes. BMC Bioinformatics 2010;11(1):320.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.1
, pp. 320
-
-
Piippo, M.1
Lietzen, N.2
Nevalainen, O.S.3
-
49
-
-
37549048173
-
Specificity rule discovery in HIV-1 protease cleavage site analysis
-
Kim H, Zhang Y, Heo YS, etal. Specificity rule discovery in HIV-1 protease cleavage site analysis. Comput Biol Chem 2008;32(1):72-79.
-
(2008)
Comput Biol Chem
, vol.32
, Issue.1
, pp. 72-79
-
-
Kim, H.1
Zhang, Y.2
Heo, Y.S.3
-
50
-
-
33847182426
-
Neuro-fuzzy prediction of biological activity and rule extraction for HIV-1 protease inhibitors
-
Andonie R, Fabry-Asztalos L, Collar CJ, et al. Neuro-fuzzy prediction of biological activity and rule extraction for HIV-1 protease inhibitors. Computational Intelligence in Bioinformatics and Computational Biology, 2005. CIBCB'05. Proceedings of the 2005 IEEE Symposium on IEEE. La Jolla, CA, USA: IEEE, 2005;1-8.
-
(2005)
Computational Intelligence in Bioinformatics and Computational Biology, 2005. CIBCB'05. Proceedings of the 2005 IEEE Symposium on IEEE. La Jolla, CA, USA: IEEE
, pp. 1-8
-
-
Andonie, R.1
Fabry-Asztalos, L.2
Collar, C.J.3
-
51
-
-
0033044637
-
Machine learning approaches for the prediction of signal peptides and other protein sorting signals
-
Nielsen H, Brunak S, Von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng 1999;12(1):3.
-
(1999)
Protein Eng
, vol.12
, Issue.1
, pp. 3
-
-
Nielsen, H.1
Brunak, S.2
Von Heijne, G.3
-
52
-
-
0037316242
-
A profile hidden markov model for signal peptides generated by hmmer
-
Zhang Z, Wood WI. A profile hidden markov model for signal peptides generated by hmmer. Bioinformatics 2003; 19(2):307.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 307
-
-
Zhang, Z.1
Wood, W.I.2
-
53
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR. Profile hidden Markov models. Bioinformatics 1998;14(9):755.
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 755
-
-
Eddy, S.R.1
-
55
-
-
20744453541
-
Biological applications of support vector machines
-
Yang ZR. Biological applications of support vector machines. Briefings Bioinformatics 2004;5(4):328.
-
(2004)
Briefings Bioinformatics
, vol.5
, Issue.4
, pp. 328
-
-
Yang, Z.R.1
-
56
-
-
77951972791
-
Cascleave: towards more accurate prediction of caspase substrate cleavage sites
-
Song J, Tan H, Shen H, et al. Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics 2010;26(6):752.
-
(2010)
Bioinformatics
, vol.26
, Issue.6
, pp. 752
-
-
Song, J.1
Tan, H.2
Shen, H.3
-
57
-
-
24744435534
-
Kernel methods for predicting protein-protein interactions
-
Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics 2005;21(Suppl. 1):i38.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Ben-Hur, A.1
Noble, W.S.2
-
58
-
-
0036358995
-
The spectrum kernel: A string kernel for svm protein classification
-
Hawaii USA: World Scientific Press
-
Leslie C, Eskin E, Noble WS. The spectrum kernel: A string kernel for svm protein classification. In Proceedings of the Pacific Symposium on Biocomputing, Vol. 7. Hawaii, USA: World Scientific Press, 2002, 566-75.
-
(2002)
Proceedings of the Pacific Symposium on Biocomputing
, vol.7
, pp. 566-575
-
-
Leslie, C.1
Eskin, E.2
Noble, W.S.3
-
59
-
-
77954481626
-
Prediction of protease substrates using sequence and structure features
-
Barkan DT, Hostetter DR, Mahrus S, et al. Prediction of protease substrates using sequence and structure features. Bioinformatics 2010;26:1714.
-
(2010)
Bioinformatics
, vol.26
, pp. 1714
-
-
Barkan, D.T.1
Hostetter, D.R.2
Mahrus, S.3
-
60
-
-
8844263749
-
A statistical framework for genomic data fusion
-
Lanckriet G.R.G, De Bie T, Cristianini N, et al. A statistical framework for genomic data fusion. Bioinformatics 2004; 20(16):2626-635.
-
(2004)
Bioinformatics
, vol.20
, Issue.16
, pp. 2626-2635
-
-
Lanckriet, G.R.G.1
De Bie, T.2
Cristianini, N.3
-
61
-
-
0036161011
-
Choosing multiple parameters for support vector machines
-
Chapelle O, Vapnik V, Bousquet O, et al. Choosing multiple parameters for support vector machines. Machine Learning 2002;46(1):131-59.
-
(2002)
Machine Learning
, vol.46
, Issue.1
, pp. 131-159
-
-
Chapelle, O.1
Vapnik, V.2
Bousquet, O.3
-
65
-
-
79955395083
-
Gps-ccd: A novel computational program for the prediction of calpain cleavage sites
-
Liu Z, Cao J, Gao X, et al. Gps-ccd: A novel computational program for the prediction of calpain cleavage sites. PLoS One 2011;6(4):e19001.
-
(2011)
PLoS One
, vol.6
, Issue.4
-
-
Liu, Z.1
Cao, J.2
Gao, X.3
-
66
-
-
49949090353
-
Penalized feature selection and classification in bioinformatics
-
Ma S, Huang J. Penalized feature selection and classification in bioinformatics. Briefings Bioinformatics 2008;9(5): 392.
-
(2008)
Briefings Bioinformatics
, vol.9
, Issue.5
, pp. 392
-
-
Ma, S.1
Huang, J.2
-
67
-
-
0036300868
-
Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent product formation
-
Peters B, Janek K, Kuckelkorn U, et al. Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent product formation. JMol Biol 2002;318(3): 847-62.
-
(2002)
JMol Biol
, vol.318
, Issue.3
, pp. 847-862
-
-
Peters, B.1
Janek, K.2
Kuckelkorn, U.3
|