-
1
-
-
3242884966
-
High-throughput docking as a source of novel drug leads
-
Alvarez, J. C. High-throughput docking as a source of novel drug leads. Curr. Opin. Chem. Biol. 2004, 8, 365-370.
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, pp. 365-370
-
-
Alvarez, J.C.1
-
2
-
-
0037032835
-
The protein kinase complement of the human genome
-
Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome. Science 2002, 298, 1912-1934.
-
(2002)
Science
, vol.298
, pp. 1912-1934
-
-
Manning, G.1
Whyte, D.B.2
Martinez, R.3
Hunter, T.4
Sudarsanam, S.5
-
3
-
-
0036527429
-
Protein kinases - The major drug targets of the twenty-first century?
-
Cohen, P. Protein kinases - the major drug targets of the twenty-first century? Nat. Rev. Drug Discov. 2002, 1, 309-315.
-
(2002)
Nat. Rev. Drug Discov.
, vol.1
, pp. 309-315
-
-
Cohen, P.1
-
4
-
-
0037392942
-
The specificities of protein kinase inhibitors: An update
-
Bain, J.; McLauchlan, H.; Elliott, M.; Cohen, P. The specificities of protein kinase inhibitors: an update. Biochem. J. 2003, 371, 199-204.
-
(2003)
Biochem. J.
, vol.371
, pp. 199-204
-
-
Bain, J.1
McLauchlan, H.2
Elliott, M.3
Cohen, P.4
-
5
-
-
4644248792
-
Recent advances in the design of matrix metalloprotease inhibitors
-
Matter, H.; Schudok, M. Recent advances in the design of matrix metalloprotease inhibitors. Curr. Opin. Drug Discov. Devel. 2004, 7, 513-535.
-
(2004)
Curr. Opin. Drug Discov. Devel.
, vol.7
, pp. 513-535
-
-
Matter, H.1
Schudok, M.2
-
6
-
-
0035028658
-
Strategies for the inhibition of serine proteases
-
Walker, B.; Lynas, J. F. Strategies for the inhibition of serine proteases. Cell. Mol. Life Sci. 2001, 58, 596-624.
-
(2001)
Cell. Mol. Life Sci.
, vol.58
, pp. 596-624
-
-
Walker, B.1
Lynas, J.F.2
-
7
-
-
1542573352
-
The pursuit of differentiated ligands for the glucocorticoid receptor
-
Coghlan, M. J.; Elmore, S. W.; Kym, P. R.; Kort, M. E. The pursuit of differentiated ligands for the glucocorticoid receptor. Curr. Top Med. Chem. 2003, 3, 1617-1635.
-
(2003)
Curr. Top Med. Chem.
, vol.3
, pp. 1617-1635
-
-
Coghlan, M.J.1
Elmore, S.W.2
Kym, P.R.3
Kort, M.E.4
-
8
-
-
1642345577
-
Protein structure prediction in structure based drug design
-
Takeda-Shitaka, M.; Takaya, D.; Chiba, C.; Tanaka, H.; Umeyama, H. Protein structure prediction in structure based drug design. Curr. Med. Chem. 2004, 11, 551-558.
-
(2004)
Curr. Med. Chem.
, vol.11
, pp. 551-558
-
-
Takeda-Shitaka, M.1
Takaya, D.2
Chiba, C.3
Tanaka, H.4
Umeyama, H.5
-
9
-
-
0029587166
-
A method to predict functional residues in proteins
-
Casari, G., Sander, C.; Valencia, A. A method to predict functional residues in proteins. Nat. Struct. Biol. 1995, 2, 171-178.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 171-178
-
-
Casari, G.1
Sander, C.2
Valencia, A.3
-
10
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge, O.; Bourne, H. R.; Cohen, F. E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 1996, 257, 342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
11
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli, S. S.; Russell, R. B. Analysis and prediction of functional sub-types from protein sequence alignments. J. Mol. Biol. 2000, 303, 61-76.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russell, R.B.2
-
12
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S. R. Profile hidden Markov models. Bioinformatics 1998, 14, 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
13
-
-
0036352010
-
Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors
-
Mirny, L. A.; Gelfand, M. S. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J. Mol. Biol. 2002, 321, 7-20.
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 7-20
-
-
Mirny, L.A.1
Gelfand, M.S.2
-
14
-
-
18144444203
-
Using orthologous and paralogous proteins to identify specificity determining residues
-
PREPRINT0002
-
Mirny, L. A.; Gelfand, M. S. Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biol. 2002, 3, PREPRINT0002.
-
(2002)
Genome Biol.
, vol.3
-
-
Mirny, L.A.1
Gelfand, M.S.2
-
16
-
-
0033580833
-
Effector recognition by the small GTP-binding proteins Ras and Ral
-
Bauer, B.; Mirey, G.; Vetter, I. R.; Garcia-Ranea, J. A.; Valencia, A. et al. Effector recognition by the small GTP-binding proteins Ras and Ral. J. Biol. Chem. 1999, 274, 17763-17770.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 17763-17770
-
-
Bauer, B.1
Mirey, G.2
Vetter, I.R.3
Garcia-Ranea, J.A.4
Valencia, A.5
-
17
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon, A.; Graur, D.; Ben-Tal, N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 2001, 307, 447-463.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
18
-
-
0032711731
-
Analysis of heregulin symmetry by weighted evolutionary tracing
-
Landgraf, R.; Fischer, D.; Eisenberg, D. Analysis of heregulin symmetry by weighted evolutionary tracing. Protein Eng. 1999, 12, 943-951.
-
(1999)
Protein Eng.
, vol.12
, pp. 943-951
-
-
Landgraf, R.1
Fischer, D.2
Eisenberg, D.3
-
19
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf, R.; Xenarios, I.; Eisenberg, D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol. 2001, 307, 1487-1502.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
20
-
-
0037423759
-
An accurate, sensitive, and scalable method to identify functional sites in protein structures
-
Yao, H.; Kristensen, D. M.; Mihalek, I.; Sowa, M. E.; Shaw, C. et al. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J. Mol. Biol. 2003, 326, 255-261.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 255-261
-
-
Yao, H.1
Kristensen, D.M.2
Mihalek, I.3
Sowa, M.E.4
Shaw, C.5
-
21
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko, T.; Bell, R. E.; Mayrose, I.; Glaser, F.; Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 2002, 18 Suppl 1, S71-77.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
22
-
-
0035910063
-
Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus kinases
-
Al-Lazikani, B.; Sheinerman, F. B.; Honig, B. Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases. Proc. Natl. Acad. Sci. USA 2001, 98, 14796-14801.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 14796-14801
-
-
Al-Lazikani, B.1
Sheinerman, F.B.2
Honig, B.3
-
23
-
-
4444314569
-
Determinants of functionality in the ubiquitin conjugating enzyme family
-
Winn, P. J.; Religa, T. L.; Battey, J. N.; Banerjee, A.; Wade, R. C. Determinants of functionality in the ubiquitin conjugating enzyme family. Structure (Camb) 2004, 12, 1563-1574.
-
(2004)
Structure (Camb)
, vol.12
, pp. 1563-1574
-
-
Winn, P.J.1
Religa, T.L.2
Battey, J.N.3
Banerjee, A.4
Wade, R.C.5
-
24
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B.; Nicholls, A. Classical electrostatics in biology and chemistry. Science 1995, 268, 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
25
-
-
4444227242
-
Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites
-
Basu, G.; Sivanesan, D.; Kawabata, T.; Go, N. Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites. J. Mol. Biol. 2004, 342, 1053-1066.
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 1053-1066
-
-
Basu, G.1
Sivanesan, D.2
Kawabata, T.3
Go, N.4
-
26
-
-
0028452896
-
A search for specificity in DNA-drug interactions
-
Cruciani, G.; Goodford, P. J. A search for specificity in DNA-drug interactions. J. Mol. Graph. 1994, 12, 116-129.
-
(1994)
J. Mol. Graph.
, vol.12
, pp. 116-129
-
-
Cruciani, G.1
Goodford, P.J.2
-
27
-
-
0028800937
-
A novel strategy for improving ligand selectivity in receptor-based drug design
-
Pastor, M.; Cruciani, G. A novel strategy for improving ligand selectivity in receptor-based drug design. J. Med. Chem. 1995, 38, 4637-4647.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 4637-4647
-
-
Pastor, M.1
Cruciani, G.2
-
28
-
-
0034632795
-
GRID/CPCA: A new computational tool to design selective ligands
-
Kastenholz, M. A.; Pastor, M.; Cruciani, G.; Haaksma, E. E.; Fox, T. GRID/CPCA: a new computational tool to design selective ligands. J. Med. Chem. 2000, 43, 3033-3044.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 3033-3044
-
-
Kastenholz, M.A.1
Pastor, M.2
Cruciani, G.3
Haaksma, E.E.4
Fox, T.5
-
29
-
-
0037030707
-
Structural Classification of Protein Kinases Using 3D Molecular Interaction Field Analysis of Their Ligand Binding Sites: Target Family Landscapes
-
Naumann, T.; Matter, H. Structural Classification of Protein Kinases Using 3D Molecular Interaction Field Analysis of Their Ligand Binding Sites: Target Family Landscapes. J. Med. Chem. 2002, 45, 2366-2378.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 2366-2378
-
-
Naumann, T.1
Matter, H.2
-
30
-
-
0346962971
-
Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions
-
Deng, Z.; Chuaqui, C.; Singh, J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem. 2004, 47, 337-344.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 337-344
-
-
Deng, Z.1
Chuaqui, C.2
Singh, J.3
-
31
-
-
12144249613
-
Interaction Profiles of Protein Kinase-Inhibitor Complexes and Their Application to Virtual Screening
-
Chuaqui, C.; Deng, Z.; Singh, J. Interaction Profiles of Protein Kinase-Inhibitor Complexes and Their Application to Virtual Screening. J. Med. Chem. 2005, 48, 121-133.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 121-133
-
-
Chuaqui, C.1
Deng, Z.2
Singh, J.3
-
32
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
-
33
-
-
17144414125
-
Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA
-
Wang, J.; Kang, X.; Kuntz, I. D.; Kollman, P. A. Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. J. Med. Chem. 2005, 48, 2432-2444.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2432-2444
-
-
Wang, J.1
Kang, X.2
Kuntz, I.D.3
Kollman, P.A.4
-
34
-
-
2542586266
-
A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations
-
Rizzo, R. C.; Toba, S.; Kuntz, I. D. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations. J. Med. Chem. 2004, 47, 3065-3074.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3065-3074
-
-
Rizzo, R.C.1
Toba, S.2
Kuntz, I.D.3
-
35
-
-
1442300070
-
Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody
-
Laitinen, T.; Kankare, J. A.; Perakyla, M. Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody. Proteins 2004, 55, 34-43.
-
(2004)
Proteins
, vol.55
, pp. 34-43
-
-
Laitinen, T.1
Kankare, J.A.2
Perakyla, M.3
-
36
-
-
0037079570
-
Computational alanine scanning of the 1:1 human growth hormone-receptor complex
-
Huo, S.; Massova, I.; Kollman, P. A. Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J. Comput. Chem. 2002, 23, 15-27.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 15-27
-
-
Huo, S.1
Massova, I.2
Kollman, P.A.3
-
37
-
-
0029000922
-
Prediction of drug binding affinities by comparative binding energy analysis
-
Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of drug binding affinities by comparative binding energy analysis. J. Med. Chem. 1995, 38, 2681-2691.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
38
-
-
0024491426
-
Recent advances in comparative molecular field analysis (CoMFA)
-
Cramer, R. D., 3rd; Patterson, D. E.; Bunce, J. D. Recent advances in comparative molecular field analysis (CoMFA). Prog. Clin. Biol. Res. 1989, 291, 161-165.
-
(1989)
Prog. Clin. Biol. Res.
, vol.291
, pp. 161-165
-
-
Cramer III, R.D.1
Patterson, D.E.2
Bunce, J.D.3
-
39
-
-
0027944195
-
Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
-
Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem. 1994, 37, 4130-4146.
-
(1994)
J. Med. Chem.
, vol.37
, pp. 4130-4146
-
-
Klebe, G.1
Abraham, U.2
Mietzner, T.3
-
40
-
-
15244361633
-
3D-QSAR CoMFA studies on trypsin-like serine protease inhibitors: A comparative selectivity analysis
-
Bhongade, B. A.; Gouripur, V. V.; Gadad, A. K. 3D-QSAR CoMFA studies on trypsin-like serine protease inhibitors: a comparative selectivity analysis. Bioorg. Med. Chem. 2005, 13, 2773-2782.
-
(2005)
Bioorg. Med. Chem.
, vol.13
, pp. 2773-2782
-
-
Bhongade, B.A.1
Gouripur, V.V.2
Gadad, A.K.3
-
41
-
-
0037920567
-
Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa
-
Bohm, M.; St rzebecher, J.; Klebe, G. Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa. J. Med. Chem. 1999, 42, 458-477.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 458-477
-
-
Bohm, M.1
Strzebecher, J.2
Klebe, G.3
-
42
-
-
14544300624
-
Matrix metalloproteinase inhibitors: A review on pharmacophore mapping and (Q)SARs results
-
Kontogiorgis, C. A.; Papaioannou, P.; Hadjipavlou-Litina, D. J. Matrix metalloproteinase inhibitors: a review on pharmacophore mapping and (Q)SARs results. Curr. Med. Chem. 2005, 12, 339-355.
-
(2005)
Curr. Med. Chem.
, vol.12
, pp. 339-355
-
-
Kontogiorgis, C.A.1
Papaioannou, P.2
Hadjipavlou-Litina, D.J.3
-
43
-
-
0242577782
-
CoMFA and docking study of novel estrogen receptor subtype selective ligands
-
Wolohan, P.; Reichert, D. E. CoMFA and docking study of novel estrogen receptor subtype selective ligands. J. Comput. Aided Mol. Des. 2003, 17, 313-328.
-
(2003)
J. Comput. Aided Mol. Des.
, vol.17
, pp. 313-328
-
-
Wolohan, P.1
Reichert, D.E.2
-
44
-
-
0141566733
-
Selectivity fields: Comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors
-
Baskin, II; Tikhonova, I. G.; Palyulin, V. A.; Zefirov, N. S. Selectivity fields: comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors. J. Med. Chem. 2003, 46, 4063-4069.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 4063-4069
-
-
Baskin, I.I.1
Tikhonova, I.G.2
Palyulin, V.A.3
Zefirov, N.S.4
-
45
-
-
0038339419
-
Genomic analysis of the eukaryotic protein kinase superfamily: A perspective
-
Hanks, S. K. Genomic analysis of the eukaryotic protein kinase superfamily: a perspective. Genome Biol. 2003, 4, 111.
-
(2003)
Genome Biol.
, vol.4
, pp. 111
-
-
Hanks, S.K.1
-
46
-
-
1542358841
-
Kinomics - Structural biology and chemogenomics of kinase inhibitors and targets
-
Vieth, M.; Higgs, R. E.; Robertson, D. H.; Shapiro, M.; Gragg, E. A. et al. Kinomics - structural biology and chemogenomics of kinase inhibitors and targets. Biochim. Biophys. Acta 2004, 1697, 243-257.
-
(2004)
Biochim. Biophys. Acta
, vol.1697
, pp. 243-257
-
-
Vieth, M.1
Higgs, R.E.2
Robertson, D.H.3
Shapiro, M.4
Gragg, E.A.5
-
47
-
-
0032530336
-
Structural basis of inhibitor selectivity in map kinases
-
Wang, Z.; Canagarajan, B. J.; Boehm, J. C.; Kassisa, S.; Cobb, M. H. et al. Structural basis of inhibitor selectivity in map kinases. Structure 1998, 6, 1117-1128.
-
(1998)
Structure
, vol.6
, pp. 1117-1128
-
-
Wang, Z.1
Canagarajan, B.J.2
Boehm, J.C.3
Kassisa, S.4
Cobb, M.H.5
-
48
-
-
10744227768
-
Acquisition of sensitivity of stress-activated protein kinases to the p38 inhibitor, sb 203580, by alteration of one or more amino acids within the atp binding pocket
-
Gum, R. J.; McLaughlin, M. M.; Kumar, S.; Wang, Z.; Bower, M. J. et al. Acquisition of sensitivity of stress-activated protein kinases to the p38 inhibitor, sb 203580, by alteration of one or more amino acids within the atp binding pocket. J. Biol. Chem. 1998, 273, 15605-15610.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 15605-15610
-
-
Gum, R.J.1
McLaughlin, M.M.2
Kumar, S.3
Wang, Z.4
Bower, M.J.5
-
49
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
50
-
-
0031043030
-
The mitochondrial carnitine palmitoyltransferase system. From concept to molecular analysis
-
McGarry, J. D.; Brown, N. F. The mitochondrial carnitine palmitoyltransferase system. From concept to molecular analysis. Eur. J. Biochem. 1997, 244, 1-14.
-
(1997)
Eur. J. Biochem.
, vol.244
, pp. 1-14
-
-
McGarry, J.D.1
Brown, N.F.2
-
51
-
-
0027418315
-
Cloning,sequencing, and expression of a cDNA encoding rat liver carnitine palmitoyltransferase I. Direct evidence that a single polypeptide is involved in inhibitor interaction and catalytic function
-
Esser, V.; Britton, C. H.; Weis, B. C.; Foster, D. W.; McGarry, J. D. Cloning,sequencing, and expression of a cDNA encoding rat liver carnitine palmitoyltransferase I. Direct evidence that a single polypeptide is involved in inhibitor interaction and catalytic function. J. Biol. Chem. 1993, 268, 5817-5822.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 5817-5822
-
-
Esser, V.1
Britton, C.H.2
Weis, B.C.3
Foster, D.W.4
McGarry, J.D.5
-
52
-
-
0028902957
-
High expression of a novel carnitine palmitoyltransferase I like protein in rat brown adipose tissue and heart: Isolation and characterization of its cDNA clone
-
Yamazaki, N.; Shinohara, Y.; Shima, A.; Terada, H. High expression of a novel carnitine palmitoyltransferase I like protein in rat brown adipose tissue and heart: isolation and characterization of its cDNA clone. FEBS Lett. 1995, 363, 41-45.
-
(1995)
FEBS Lett.
, vol.363
, pp. 41-45
-
-
Yamazaki, N.1
Shinohara, Y.2
Shima, A.3
Terada, H.4
-
53
-
-
0036421318
-
A novel brain-expressed protein related to carnitine palmitoyltransferase I
-
Price, N. T.; van der Leij, F. R.; Jackson, V. N.; Corstorphine, C. G.; Thomson, R. et al. A novel brain-expressed protein related to carnitine palmitoyltransferase I. Genomics 2002, 80, 433-442.
-
(2002)
Genomics
, vol.80
, pp. 433-442
-
-
Price, N.T.1
van der Leij, F.R.2
Jackson, V.N.3
Corstorphine, C.G.4
Thomson, R.5
-
54
-
-
0019864083
-
Carnitine acyltransferases in rat liver peroxisomes
-
Bieber, L. L.; Krahling, J. B.; Clarke, P. R.; Valkner, K. J.; Tolbert, N. E. Carnitine acyltransferases in rat liver peroxisomes. Arch. Biochem. Biophys. 1981, 211, 599-604.
-
(1981)
Arch. Biochem. Biophys.
, vol.211
, pp. 599-604
-
-
Bieber, L.L.1
Krahling, J.B.2
Clarke, P.R.3
Valkner, K.J.4
Tolbert, N.E.5
-
55
-
-
0023893052
-
Carnitine
-
Bieber, L. L. Carnitine. Ann Rev Biochem 1988, 57, 261-283.
-
(1988)
Ann Rev Biochem
, vol.57
, pp. 261-283
-
-
Bieber, L.L.1
-
56
-
-
0032777703
-
Carnitine acyltransferases: Functional significance of subcellular distribution and membrane topology
-
Zammit, V. A. Carnitine acyltransferases: functional significance of subcellular distribution and membrane topology. Prog. Lipid Res. 1999, 38, 199-224.
-
(1999)
Prog. Lipid Res.
, vol.38
, pp. 199-224
-
-
Zammit, V.A.1
-
57
-
-
0032544596
-
Redesign of Choline Acetyltransferase Specificity by Protein Engineering
-
Cronin, C. N. Redesign of Choline Acetyltransferase Specificity by Protein Engineering. J. Biol. Chem. 1998, 273, 24465-24469.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 24465-24469
-
-
Cronin, C.N.1
-
58
-
-
0037646548
-
Identification of Conserved Amino Acid Residues in Rat Liver Carnitine Palmitoyltransferase I Critical for Malonyl-CoA Inhibition
-
Morillas, M.; Gomez-Puertas, P.; Bentebibel, A.; Selles, E.; Casals, N. et al. Identification of Conserved Amino Acid Residues in Rat Liver Carnitine Palmitoyltransferase I Critical for Malonyl-CoA Inhibition. J. Biol. Chem. 2003, 278, 9058-9063.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 9058-9063
-
-
Morillas, M.1
Gomez-Puertas, P.2
Bentebibel, A.3
Selles, E.4
Casals, N.5
-
59
-
-
0002832714
-
Comparative analysis of different methods for the detection of specificity regions in protein families
-
D. Lundh, Olsson, B., Narayanan A., ed. (Singapore, New Jersey, London, Hong Kong, World Scientific)
-
Pazos, F.; Sanchez-Pulido, L.; García-Ranea, J. A.; Andrade, M. A.; Atrian, S. et al. (1997). Comparative analysis of different methods for the detection of specificity regions in protein families. In Biocomputing and Emergent Computation, D. Lundh, Olsson, B., Narayanan A., ed. (Singapore, New Jersey, London, Hong Kong, World Scientific), pp. 132-145.
-
(1997)
Biocomputing and Emergent Computation
, pp. 132-145
-
-
Pazos, F.1
Sanchez-Pulido, L.2
García-Ranea, J.A.3
Andrade, M.A.4
Atrian, S.5
-
60
-
-
0037470597
-
Automatic methods for predicting functionally important residues
-
del Sol, A.; Pazos, F.; Valencia, A. Automatic methods for predicting functionally important residues. J. Mol. Biol. 2003, 326, 1289-1302.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1289-1302
-
-
del Sol, A.1
Pazos, F.2
Valencia, A.3
-
61
-
-
12744280700
-
Alteration of the malonyl-CoA/carnitine palmitoyltransferase I interaction in the beta-cell impairs glucose-induced insulin secretion
-
Herrero, L.; Rubi, B.; Sebastian, D.; Serra, D.; Asins, G. et al. Alteration of the malonyl-CoA/carnitine palmitoyltransferase I interaction in the beta-cell impairs glucose-induced insulin secretion. Diabetes 2005, 54, 462-471.
-
(2005)
Diabetes
, vol.54
, pp. 462-471
-
-
Herrero, L.1
Rubi, B.2
Sebastian, D.3
Serra, D.4
Asins, G.5
-
62
-
-
0035976911
-
Structural model of the catalytic core of carnitine palmitoyltransferase I and carnitine octanoyltransferase (COT): Mutation of CPT I histidine 473 and alanine 381 and COT alanine 238 impairs the catalytic activity
-
Morillas, M.; Gomez-Puertas, P.; Roca, R.; Serra, D.; Asins, G. et al. Structural model of the catalytic core of carnitine palmitoyltransferase I and carnitine octanoyltransferase (COT): mutation of CPT I histidine 473 and alanine 381 and COT alanine 238 impairs the catalytic activity. J. Biol. Chem. 2001, 276, 45001-45008.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 45001-45008
-
-
Morillas, M.1
Gomez-Puertas, P.2
Roca, R.3
Serra, D.4
Asins, G.5
-
63
-
-
2542614421
-
Structural model of carnitine palmitoyltransferase I based on the carnitine acetyltransferase crystal
-
Morillas, M.; Lopez-Viñas, E.; Valencia, A.; Serra, D.; Gomez-Puertas, P. et al. Structural model of carnitine palmitoyltransferase I based on the carnitine acetyltransferase crystal. Biochem. J. 2004, 379, 777-784.
-
(2004)
Biochem. J.
, vol.379
, pp. 777-784
-
-
Morillas, M.1
Lopez-Viñas, E.2
Valencia, A.3
Serra, D.4
Gomez-Puertas, P.5
-
64
-
-
0037192836
-
Structural model of a malonyl-CoA-binding site of carnitine octanoyltransferase and carnitine palmitoyltransferase I: Mutational analysis of a malonyl-CoA affinity domain
-
Morillas, M.; Gomez-Puertas, P.; Rubi, B.; Clotet, J.; Arino, J. et al. Structural model of a malonyl-CoA-binding site of carnitine octanoyltransferase and carnitine palmitoyltransferase I: mutational analysis of a malonyl-CoA affinity domain. J. Biol. Chem. 2002, 277, 11473-11480.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 11473-11480
-
-
Morillas, M.1
Gomez-Puertas, P.2
Rubi, B.3
Clotet, J.4
Arino, J.5
-
65
-
-
4043096944
-
Redesign of carnitine acetyltransferase specificity by protein engineering
-
Cordente, A. G.; Lopez-Vinas, E.; Vazquez, M. I.; Swiegers, J. H.; Pretorius, I. S. et al. Redesign of carnitine acetyltransferase specificity by protein engineering. J. Biol. Chem. 2004, 279, 33899-33908.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 33899-33908
-
-
Cordente, A.G.1
Lopez-Vinas, E.2
Vazquez, M.I.3
Swiegers, J.H.4
Pretorius, I.S.5
-
66
-
-
0034470147
-
Sequence determinants of function and evolution in serine proteases
-
Krem, M. M.; Rose, T.; Di Cera, E. Sequence determinants of function and evolution in serine proteases. Trends Cardiovasc. Med. 2000, 10, 171-176.
-
(2000)
Trends Cardiovasc. Med.
, vol.10
, pp. 171-176
-
-
Krem, M.M.1
Rose, T.2
Di Cera, E.3
-
67
-
-
0032510317
-
Comparative binding energy analysis of HIV-1 protease inhibitors: Incorporation of solvent effects and validation as a powerful tool in receptor-based drug design
-
Perez, C.; Pastor, M.; Ortiz, A. R.; Gago, F. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. J. Med. Chem. 1998, 41, 836-852.
-
(1998)
J. Med. Chem.
, vol.41
, pp. 836-852
-
-
Perez, C.1
Pastor, M.2
Ortiz, A.R.3
Gago, F.4
-
68
-
-
0036208872
-
Recent progress in multiple sequence alignment: A survey
-
Notredame, C. Recent progress in multiple sequence alignment: a survey. Pharmacogenomics 2002, 3, 131-144.
-
(2002)
Pharmacogenomics
, vol.3
, pp. 131-144
-
-
Notredame, C.1
-
70
-
-
0035984476
-
Local weighting schemes for protein multiple sequence alignment
-
Heringa, J. Local weighting schemes for protein multiple sequence alignment. Comput. Chem. 2002, 26, 459-477.
-
(2002)
Comput. Chem.
, vol.26
, pp. 459-477
-
-
Heringa, J.1
-
71
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
O'Sullivan, O.; Suhre, K.; Abergel, C.; Higgins, D. G.; Notredame, C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 2004, 340, 385-395.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
72
-
-
0038460858
-
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
-
McGovern, S. L.; Shoichet, B. K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem. 2003, 46, 2895-2907.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 2895-2907
-
-
McGovern, S.L.1
Shoichet, B.K.2
-
73
-
-
0242330730
-
Assessment of homology-based predictions in CASP5
-
Tramontano, A.; Morea, V. Assessment of homology-based predictions in CASP5. Proteins 2003, 53 Suppl 6, 352-368.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 352-368
-
-
Tramontano, A.1
Morea, V.2
-
74
-
-
0037414421
-
In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling
-
Contreras-Moreira, B.; Fitzjohn, P. W.; Bates, P. A. In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J. Mol. Biol. 2003, 328, 593-608.
-
(2003)
J. Mol. Biol.
, vol.328
, pp. 593-608
-
-
Contreras-Moreira, B.1
Fitzjohn, P.W.2
Bates, P.A.3
-
75
-
-
1842559320
-
Alignment of protein sequences by their profiles
-
Marti-Renom, M. A.; Madhusudhan, M. S.; Sali, A. Alignment of protein sequences by their profiles. Protein Sci. 2004, 13, 1071-1087.
-
(2004)
Protein Sci.
, vol.13
, pp. 1071-1087
-
-
Marti-Renom, M.A.1
Madhusudhan, M.S.2
Sali, A.3
-
76
-
-
7444236378
-
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
-
Qian, B.; Ortiz, A. R.; Baker, D. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc. Natl. Acad. Sci. USA 2004, 101, 15346-15351.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 15346-15351
-
-
Qian, B.1
Ortiz, A.R.2
Baker, D.3
-
77
-
-
0242301182
-
Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials
-
Evers, A.; Gohlke, H.; Klebe, G. Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. J. Mol. Biol. 2003, 334, 327-345.
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 327-345
-
-
Evers, A.1
Gohlke, H.2
Klebe, G.3
-
78
-
-
0347123444
-
Ligand-supported homology modeling of g-protein-coupled receptor sites: Models sufficient for successful virtual screening
-
Evers, A.; Klebe, G. Ligand-supported homology modeling of g-protein-coupled receptor sites: models sufficient for successful virtual screening. Angew. Chem. Int. Ed. Engl. 2004, 43, 248-251.
-
(2004)
Angew. Chem. Int. Ed. Engl.
, vol.43
, pp. 248-251
-
-
Evers, A.1
Klebe, G.2
-
79
-
-
6044260116
-
Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model
-
Evers, A.; Klebe, G. Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model. J. Med. Chem. 2004, 47, 5381-5392.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 5381-5392
-
-
Evers, A.1
Klebe, G.2
-
80
-
-
4744365803
-
Soft docking and multiple receptor conformations in virtual screening
-
Ferrari, A. M.; Wei, B. Q.; Costantino, L.; Shoichet, B. K. Soft docking and multiple receptor conformations in virtual screening. J. Med. Chem. 2004, 47, 5076-5084.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 5076-5084
-
-
Ferrari, A.M.1
Wei, B.Q.2
Costantino, L.3
Shoichet, B.K.4
-
81
-
-
0036298514
-
Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility
-
Zoete, V.; Michielin, O.; Karplus, M. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J. Mol. Biol. 2002, 315, 21-52.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 21-52
-
-
Zoete, V.1
Michielin, O.2
Karplus, M.3
-
82
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M.; McCammon, J. A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 2002, 9, 646-652.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
83
-
-
1642365068
-
New advances in normal mode analysis of supermolecular complexes and applications to structural refinement
-
Ma, J. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr. Protein Pept. Sci. 2004, 5, 119-123.
-
(2004)
Curr. Protein Pept. Sci.
, vol.5
, pp. 119-123
-
-
Ma, J.1
-
84
-
-
15244353539
-
Side-chain flexibility in protein-ligand binding: The minimal rotation hypothesis
-
Zavodszky, M. I.; Kuhn, L. A. Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci. 2005, 14, 1104-1114.
-
(2005)
Protein Sci.
, vol.14
, pp. 1104-1114
-
-
Zavodszky, M.I.1
Kuhn, L.A.2
-
85
-
-
1442351132
-
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
-
Cavasotto, C. N.; Abagyan, R. A. Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases. J. Mol. Biol. 2004, 337, 209-225.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
86
-
-
1842471241
-
Testing a flexible-receptor docking algorithm in a model binding site
-
Wei, B. Q.; Weaver, L. H.; Ferrari, A. M.; Matthews, B. W.; Shoichet, B. K. Testing a flexible-receptor docking algorithm in a model binding site. J. Mol. Biol. 2004, 337, 1161-1182.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 1161-1182
-
-
Wei, B.Q.1
Weaver, L.H.2
Ferrari, A.M.3
Matthews, B.W.4
Shoichet, B.K.5
-
87
-
-
6344245774
-
Incorporating protein flexibility in structure-based drug discovery: Using HIV-1 protease as a test case
-
Meagher, K. L.; Carlson, H. A. Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. J. Am. Chem. Soc. 2004, 126, 13276-13281.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 13276-13281
-
-
Meagher, K.L.1
Carlson, H.A.2
-
88
-
-
14844289540
-
Illuminating drug discovery with biological pathways
-
Apic, G.; Ignjatovic, T.; Boyer, S.; Russell, R. B. Illuminating drug discovery with biological pathways. FEBS Lett. 2005, 579, 1872-1877.
-
(2005)
FEBS Lett.
, vol.579
, pp. 1872-1877
-
-
Apic, G.1
Ignjatovic, T.2
Boyer, S.3
Russell, R.B.4
-
89
-
-
19744365702
-
A small molecule-kinase interaction map for clinical kinase inhibitors
-
Fabian, M. A.; Biggs, W. H. 3rd; Treiber, D. K.; Atteridge, C. E.; Azimioara, M. D. et al. A small molecule-kinase interaction map for clinical kinase inhibitors. Nat. Biotechnol. 2005, 23, 329-336.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 329-336
-
-
Fabian, M.A.1
Biggs III, W.H.2
Treiber, D.K.3
Atteridge, C.E.4
Azimioara, M.D.5
-
90
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna, R.; Sugawara, H.; Koike, T.; Lopez, R.; Gibson, T. J. et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003, 31, 3497-3500.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
-
91
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C.; Higgins, D. G.; Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302, 205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
92
-
-
0003845223
-
The PyMOL Molecular Graphics System
-
DeLano. DeLano Scientific LLC, San Carlos, CA, USA
-
DeLano. The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA http://wwwpymolorg.
-
-
-
|