-
2
-
-
0038270775
-
Chemogenomics knowledge-based strategies in drug discovery
-
DOI 10.1358/dnp.2003.16.2.829326
-
Jacoby E, Schuffenhauer A, Floersheim P (2003) Chemogenomics knowledge-based strategies in drug discovery. Drug News Perspect 16:93-102. (Pubitemid 36749735)
-
(2003)
Drug News and Perspectives
, vol.16
, Issue.2
, pp. 93-102
-
-
Jacoby, E.1
Schuffenhauer, A.2
Floersheim, P.3
-
3
-
-
33748751182
-
Chemogenomics: Structuring the drug discovery process to gene families
-
Harris CJ, Stevens AP (2006) Chemogenomics: structuring the drug discovery process to gene families. Drug Discov Today 11:880-888.
-
(2006)
Drug Discov Today
, vol.11
, pp. 880-888
-
-
Harris, C.J.1
Stevens, A.P.2
-
4
-
-
1542358841
-
Kinomics - Structural biology and chemogenomics of kinase inhibitors and targets
-
DOI 10.1016/j.bbapap.2003.11.028, PII S1570963903003807
-
Vieth M, Higgs RE, Robertson DH, Shapiro M, Gragg EA, Hemmerle H (2004) Kinomics-structural biology and chemogenomics of kinase inhibitors and targets. Biochim Biophys Acta 1697:243-257. (Pubitemid 38326776)
-
(2004)
Biochimica et Biophysica Acta - Proteins and Proteomics
, vol.1697
, Issue.1-2
, pp. 243-257
-
-
Vieth, M.1
Higgs, R.E.2
Robertson, D.H.3
Shapiro, M.4
Gragg, E.A.5
Hemmerle, H.6
-
5
-
-
0037803570
-
Human and mouse proteases: A comparative genomic approach
-
DOI 10.1038/nrg1111
-
Puente XS, Sanchez LM, Overall CM, Lopez-Otin C (2003) Human and mouse proteases: a comparative genomic approach. Nat Rev Genet 4:544-558. (Pubitemid 36781345)
-
(2003)
Nature Reviews Genetics
, vol.4
, Issue.7
, pp. 544-558
-
-
Puente, X.S.1
Sanchez, L.M.2
Overall, C.M.3
Lopez-Otin, C.4
-
6
-
-
33748308883
-
Targeting proteases: Successes, failures and future prospects
-
DOI 10.1038/nrd2092, PII NRD2092
-
Turk B (2006) Targeting proteases: successes, failures and future prospects. Nat Rev Drug Discov 5:785-799. (Pubitemid 44323703)
-
(2006)
Nature Reviews Drug Discovery
, vol.5
, Issue.9
, pp. 785-799
-
-
Turk, B.1
-
7
-
-
57649155302
-
Proteases: Multifunctional enzymes in life and disease
-
Lopez-Otin C, Bond JS (2008) Proteases: multifunctional enzymes in life and disease. J Biol Chem 283:30433-30437.
-
(2008)
J Biol Chem
, vol.283
, pp. 30433-30437
-
-
Lopez-Otin, C.1
Bond, J.S.2
-
8
-
-
38549096018
-
MEROPS: The peptidase database
-
Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ (2008) MEROPS: the peptidase database. Nucleic Acids Res 36:D320-D325.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Rawlings, N.D.1
Morton, F.R.2
Kok, C.Y.3
Kong, J.4
Barrett, A.J.5
-
9
-
-
0014211618
-
On the size of the active site in proteases. I. Papain
-
Schechter I, Berger A (1967) On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun 27:157-162.
-
(1967)
Biochem Biophys Res Commun
, vol.27
, pp. 157-162
-
-
Schechter, I.1
Berger, A.2
-
10
-
-
33745391215
-
Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases
-
Nidhi Glick M, Davies JW, Jenkins JL (2006) Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J Chem Inf Model 46:1124-1133.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 1124-1133
-
-
Nidhi Glick, M.1
Davies, J.W.2
Jenkins, J.L.3
-
11
-
-
2642585575
-
Role of the 17 protein in proteolytic processing of vaccinia virus membrane and core components
-
DOI 10.1128/JVI.78.12.6335-6343.2004
-
Ansarah-Sobrinho C, Moss B (2004) Role of the I7 protein in proteolytic processing of vaccinia virus membrane and core components. J Virol 78:6335-6343. (Pubitemid 38715932)
-
(2004)
Journal of Virology
, vol.78
, Issue.12
, pp. 6335-6343
-
-
Ansarah-Sobrinho, C.1
Moss, B.2
-
12
-
-
0141676552
-
Molecular dissection of the vaccinia virus I7L core protein proteinase
-
Byrd CM, Bolken TC, Hruby DE (2003) Molecular dissection of the vaccinia virus I7L core protein proteinase. J Virol 77:11279-11283.
-
(2003)
J Virol
, vol.77
, pp. 11279-11283
-
-
Byrd, C.M.1
Bolken, T.C.2
Hruby, D.E.3
-
13
-
-
0032440487
-
Bacteroides fragilis enterotoxin cleaves the zonula adherens protein, E- Cadherin
-
DOI 10.1073/pnas.95.25.14979
-
Wu S, Lim KC, Huang J, Saidi RF, Sears CL (1998) Bacteroides fragilis enterotoxin cleaves the zonula adherens protein, E-cadherin. Proc Natl Acad Sci USA 95:14979-14984. (Pubitemid 29003742)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.25
, pp. 14979-14984
-
-
Wu, S.1
Lim, K.-C.2
Huang, J.3
Saidi, R.F.4
Sears, C.L.5
-
14
-
-
56349163806
-
Enterotoxigenic Bacteroides fragilis
-
Holton J (2008) Enterotoxigenic Bacteroides fragilis. Curr Infect Dis Rep 10:99-104.
-
(2008)
Curr Infect Dis Rep
, vol.10
, pp. 99-104
-
-
Holton, J.1
-
15
-
-
32444434664
-
Caspases 3 and 7: Key mediators of mitochondrial events of apoptosis
-
DOI 10.1126/science.1115035
-
Lakhani SA, Masud A, Kuida K, Porter GA, Jr, Booth CJ, Mehal WZ, Inayat I, Flavell RA (2006) Caspases 3 and 7: key mediators of mitochondrial events of apoptosis. Science 311:847-851. (Pubitemid 43228848)
-
(2006)
Science
, vol.311
, Issue.5762
, pp. 847-851
-
-
Lakhani, S.A.1
Masud, A.2
Kuida, K.3
Porter Jr., G.A.4
Booth, C.J.5
Mehal, W.Z.6
Inayat, I.7
Flavell, R.A.8
-
16
-
-
75149167437
-
Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity
-
Demon D, Van Damme P, Vanden Berghe T, Deceuninck A, Van Durme J, Verspurten J, Helsens K, Impens F, Wejda M, Schymkowitz J, Rousseau F, Madder A, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P (2009) Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity.Mol Cell Proteomics 8:2700-2714.
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 2700-2714
-
-
Demon, D.1
Van Damme, P.2
Vanden Berghe, T.3
Deceuninck, A.4
Van Durme, J.5
Verspurten, J.6
Helsens, K.7
Impens, F.8
Wejda, M.9
Schymkowitz, J.10
Rousseau, F.11
Madder, A.12
Vandekerckhove, J.13
Declercq, W.14
Gevaert, K.15
Vandenabeele, P.16
-
17
-
-
51349139607
-
Executioner caspase-3 and caspase-7 are functionally distinct proteases
-
Walsh JG, Cullen SP, Sheridan C, Luthi AU, Gerner C, Martin SJ (2008) Executioner caspase-3 and caspase-7 are functionally distinct proteases. Proc Natl Acad Sci USA 105:12815-12819.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 12815-12819
-
-
Walsh, J.G.1
Cullen, S.P.2
Sheridan, C.3
Luthi, A.U.4
Gerner, C.5
Martin, S.J.6
-
18
-
-
0030849093
-
A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis
-
Thornberry NA, Rano TA, Peterson EP, Rasper DM, Timkey T, Garcia-Calvo M, Houtzager VM, Nordstrom PA, Roy S, Vaillancourt JP, Chapman KT, Nicholson DW (1997) A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis. J Biol Chem 272:17907-17911.
-
(1997)
J Biol Chem
, vol.272
, pp. 17907-17911
-
-
Thornberry, N.A.1
Rano, T.A.2
Peterson, E.P.3
Rasper, D.M.4
Timkey, T.5
Garcia-Calvo, M.6
Houtzager, V.M.7
Nordstrom, P.A.8
Roy, S.9
Vaillancourt, J.P.10
Chapman, K.T.11
Nicholson, D.W.12
-
19
-
-
33750984207
-
Mutation of the Myxoma virus SERP2 P1-site to prevent proteinase inhibition causes apoptosis in cultured RK-13 cells and attenuates disease in rabbits, but mutation to alter specificity causes apoptosis without reducing virulence
-
MacNeill AL, Turner PC, Moyer RW (2006) Mutation of the Myxoma virus SERP2 P1-site to prevent proteinase inhibition causes apoptosis in cultured RK-13 cells and attenuates disease in rabbits, but mutation to alter specificity causes apoptosis without reducing virulence. Virology 356:12-22.
-
(2006)
Virology
, vol.356
, pp. 12-22
-
-
MacNeill, A.L.1
Turner, P.C.2
Moyer, R.W.3
-
20
-
-
0037136033
-
Discovery of potent, selective human granzyme B inhibitors that inhibit CTL mediated apoptosis
-
Willoughby CA, Bull HG, Garcia-Calvo M, Jiang J, Chapman KT, Thornberry NA (2002) Discovery of potent, selective human granzyme B inhibitors that inhibit CTL mediated apoptosis. Bioorg Med Chem Lett 12:2197-2200.
-
(2002)
Bioorg Med Chem Lett
, vol.12
, pp. 2197-2200
-
-
Willoughby, C.A.1
Bull, H.G.2
Garcia-Calvo, M.3
Jiang, J.4
Chapman, K.T.5
Thornberry, N.A.6
-
21
-
-
67349217364
-
Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling
-
Fang B, Fu G, Agniswamy J, Harrison RW, Weber IT (2009) Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling. Apoptosis 14:741-752.
-
(2009)
Apoptosis
, vol.14
, pp. 741-752
-
-
Fang, B.1
Fu, G.2
Agniswamy, J.3
Harrison, R.W.4
Weber, I.T.5
-
22
-
-
0035026112
-
The three-dimensional structure of human granzyme B compared to caspase-3, key mediators of cell death with cleavage specificity for aspartic acid in P1
-
Rotonda J, Garcia-Calvo M, Bull HG, Geissler WM, McKeever BM, Willoughby CA, Thornberry NA, Becker JW (2001) The three-dimensional structure of human granzyme B compared to caspase-3, key mediators of cell death with cleavage specificity for aspartic acid in P1. Chem Biol 8:357-368.
-
(2001)
Chem Biol
, vol.8
, pp. 357-368
-
-
Rotonda, J.1
Garcia-Calvo, M.2
Bull, H.G.3
Geissler, W.M.4
McKeever, B.M.5
Willoughby, C.A.6
Thornberry, N.A.7
Becker, J.W.8
-
23
-
-
0034628448
-
Protease inhibitors: Current status and future prospects
-
Leung D, Abbenante G, Fairlie DP (2000) Protease inhibitors: current status and future prospects. J Med Chem 43:305-341.
-
(2000)
J Med Chem
, vol.43
, pp. 305-341
-
-
Leung, D.1
Abbenante, G.2
Fairlie, D.P.3
-
24
-
-
33845339435
-
Protease inhibitors in the clinic
-
Abbenante G, Fairlie DP (2005) Protease inhibitors in the clinic. Med Chem 1:71-104.
-
(2005)
Med Chem
, vol.1
, pp. 71-104
-
-
Abbenante, G.1
Fairlie, D.P.2
-
25
-
-
2342531089
-
Reducing the peptidyl features of caspase-3 inhibitors: A structural analysis
-
Becker JW, Rotonda J, Soisson SM, Aspiotis R, Bayly C, Francoeur S, Gallant M, Garcia-Calvo M, Giroux A, Grimm E, Han Y, McKay D, Nicholson DW, Peterson E, Renaud J, Roy S, Thornberry N, Zamboni R (2004) Reducing the peptidyl features of caspase-3 inhibitors: a structural analysis. J Med Chem 47:2466-2474.
-
(2004)
J Med Chem
, vol.47
, pp. 2466-2474
-
-
Becker, J.W.1
Rotonda, J.2
Soisson, S.M.3
Aspiotis, R.4
Bayly, C.5
Francoeur, S.6
Gallant, M.7
Garcia-Calvo, M.8
Giroux, A.9
Grimm, E.10
Han, Y.11
McKay, D.12
Nicholson, D.W.13
Peterson, E.14
Renaud, J.15
Roy, S.16
Thornberry, N.17
Zamboni, R.18
-
26
-
-
31044445704
-
Design, synthesis, and biological activity of novel factor Xa inhibitors: Improving metabolic stability by S1 and S4 ligand modification
-
Komoriya S, Kobayashi S, Osanai K, Yoshino T, Nagata T, Haginoya N, Nakamoto Y, Mochizuki A, Nagahara T, Suzuki M, Shimada T, Watanabe K, Isobe Y, Furugoori T (2006) Design, synthesis, and biological activity of novel factor Xa inhibitors: improving metabolic stability by S1 and S4 ligand modification. Bioorg Med Chem 14:1309-1330.
-
(2006)
Bioorg Med Chem
, vol.14
, pp. 1309-1330
-
-
Komoriya, S.1
Kobayashi, S.2
Osanai, K.3
Yoshino, T.4
Nagata, T.5
Haginoya, N.6
Nakamoto, Y.7
Mochizuki, A.8
Nagahara, T.9
Suzuki, M.10
Shimada, T.11
Watanabe, K.12
Isobe, Y.13
Furugoori, T.14
-
27
-
-
75549086071
-
Database systems for knowledge-based discovery
-
Jagarlapudi SA, Kishan KV (2009) Database systems for knowledge-based discovery. Methods Mol Biol 575:159-172.
-
(2009)
Methods Mol Biol
, vol.575
, pp. 159-172
-
-
Jagarlapudi, S.A.1
Kishan, K.V.2
-
28
-
-
4544350863
-
Enrichment of extremely noisy high-throughput screening data using a naive Bayes classifier
-
Glick M, Klon AE, Acklin P, Davies JW (2004) Enrichment of extremely noisy high-throughput screening data using a naive Bayes classifier. J Biomol Screen 9:32-36.
-
(2004)
J Biomol Screen
, vol.9
, pp. 32-36
-
-
Glick, M.1
Klon, A.E.2
Acklin, P.3
Davies, J.W.4
-
29
-
-
4143122120
-
Classification of kinase inhibitors using a Bayesian model
-
Xia X, Maliski EG, Gallant P, Rogers D (2004) Classification of kinase inhibitors using a Bayesian model. J Med Chem 47:4463-4470.
-
(2004)
J Med Chem
, vol.47
, pp. 4463-4470
-
-
Xia, X.1
Maliski, E.G.2
Gallant, P.3
Rogers, D.4
-
30
-
-
0032522413
-
Cathepsin L2, a novel human cysteine proteinase produced by breast and colorectal carcinomas
-
Santamaria I, Velasco G, Cazorla M, Fueyo A, Campo E, Lopez-Otin C (1998) Cathepsin L2, a novel human cysteine proteinase produced by breast and colorectal carcinomas. Cancer Res 58:1624-1630. (Pubitemid 28215082)
-
(1998)
Cancer Research
, vol.58
, Issue.8
, pp. 1624-1630
-
-
Santamaria, I.1
Velasco, G.2
Cazorla, M.3
Fueyo, A.4
Campo, E.5
Lopez-Otin, C.6
-
31
-
-
0034650486
-
Cell surface-localized matrix metalloproteinase-9 proteolytically activates TGF-beta and promotes tumor invasion and angiogenesis
-
Yu Q, Stamenkovic I (2000) Cell surface-localized matrix metalloproteinase-9 proteolytically activates TGF-beta and promotes tumor invasion and angiogenesis. Genes Dev 14:163-176.
-
(2000)
Genes Dev
, vol.14
, pp. 163-176
-
-
Yu, Q.1
Stamenkovic, I.2
-
32
-
-
0036181085
-
Pepsinogens, progastricsins, and prochymosins: Structure, function, evolution, and development
-
Kageyama T (2002) Pepsinogens, progastricsins, and prochymosins: structure, function, evolution, and development. Cell Mol Life Sci 59:288-306.
-
(2002)
Cell Mol Life Sci
, vol.59
, pp. 288-306
-
-
Kageyama, T.1
-
33
-
-
65249092595
-
Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis
-
Scheiber J, Chen B, Milik M, Sukuru SC, Bender A, Mikhailov D, Whitebread S, Hamon J, Azzaoui K, Urban L, Glick M, Davies JW, Jenkins JL (2009) Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis. J Chem Inf Model 49:308-317.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 308-317
-
-
Scheiber, J.1
Chen, B.2
Milik, M.3
Sukuru, S.C.4
Bender, A.5
Mikhailov, D.6
Whitebread, S.7
Hamon, J.8
Azzaoui, K.9
Urban, L.10
Glick, M.11
Davies, J.W.12
Jenkins, J.L.13
-
34
-
-
14044274265
-
Recent developments in the design of specific matrix metalloproteinase inhibitors aided by structural and computational studies
-
Rao BG (2005) Recent developments in the design of specific matrix metalloproteinase inhibitors aided by structural and computational studies. Curr Pharm Des 11:295-322.
-
(2005)
Curr Pharm des
, vol.11
, pp. 295-322
-
-
Rao, B.G.1
-
35
-
-
0036720561
-
The effect of prime-site occupancy on the hepatitis C virus NS3 protease structure
-
Casbarra A, Piaz FD, Ingallinella P, Orru S, Pucci P, Pessi A, Bianchi E (2002) The effect of prime-site occupancy on the hepatitis C virus NS3 protease structure. Protein Sci 11:2102-2112.
-
(2002)
Protein Sci
, vol.11
, pp. 2102-2112
-
-
Casbarra, A.1
Piaz, F.D.2
Ingallinella, P.3
Orru, S.4
Pucci, P.5
Pessi, A.6
Bianchi, E.7
-
36
-
-
33745516142
-
Probing the substrate specificity of the dengue virus type 2 NS3 serine protease by using internally quenched fluorescent peptides
-
Niyomrattanakit P, Yahorava S, Mutule I, Mutulis F, Petrovska R, Prusis P, Katzenmeier G, Wikberg JE (2006) Probing the substrate specificity of the dengue virus type 2 NS3 serine protease by using internally quenched fluorescent peptides. Biochem J 397:203-211.
-
(2006)
Biochem J
, vol.397
, pp. 203-211
-
-
Niyomrattanakit, P.1
Yahorava, S.2
Mutule, I.3
Mutulis, F.4
Petrovska, R.5
Prusis, P.6
Katzenmeier, G.7
Wikberg, J.E.8
-
37
-
-
67649617069
-
Subsite cooperativity in protease specificity
-
Ng NM, Pike RN, Boyd SE (2009) Subsite cooperativity in protease specificity. Biol Chem 390:401-407.
-
(2009)
Biol Chem
, vol.390
, pp. 401-407
-
-
Ng, N.M.1
Pike, R.N.2
Boyd, S.E.3
-
38
-
-
17244364283
-
Proteases universally recognize beta strands in their active sites
-
DOI 10.1021/cr040669e
-
Tyndall JD, Nall T, Fairlie DP (2005) Proteases universally recognize beta strands in their active sites. Chem Rev 105:973-999. (Pubitemid 40527381)
-
(2005)
Chemical Reviews
, vol.105
, Issue.3
, pp. 973-999
-
-
Tyndall, J.D.A.1
Nall, T.2
Fairlie, D.P.3
-
39
-
-
77952772341
-
Extended-connectivity fingerprints
-
Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50:742-754.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 742-754
-
-
Rogers, D.1
Hahn, M.2
-
40
-
-
17144385534
-
Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
-
Triballeau N, Acher F, Brabet I, Pin JP, Bertrand HO (2005) Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Med Chem 48:2534-2547.
-
(2005)
J Med Chem
, vol.48
, pp. 2534-2547
-
-
Triballeau, N.1
Acher, F.2
Brabet, I.3
Pin, J.P.4
Bertrand, H.O.5
-
41
-
-
0003437299
-
-
version 3.68. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
-
Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.68. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
-
(2005)
PHYLIP (Phylogeny Inference Package)
-
-
Felsenstein, J.1
-
42
-
-
47049086792
-
PhyloWidget: Web-based visualizations for the tree of life
-
Jordan GE, Piel WH (2008) PhyloWidget: web-based visualizations for the tree of life. Bioinformatics 24:1641-1642.
-
(2008)
Bioinformatics
, vol.24
, pp. 1641-1642
-
-
Jordan, G.E.1
Piel, W.H.2
|