-
1
-
-
33646008247
-
Differential targeting of Gbetagamma-Subunit signaling with small molecules
-
Bonacci, T. M.; Mathews, J. L.; Yuan, C.; Lehmann, D. M.; Malik, S.; Wu, D.; Font, J. L.; Bidlack, J. M.; Smrcka, A. V. Differential Targeting of Gbetagamma-Subunit Signaling with Small Molecules. Science 2006, 312, 443-446.
-
(2006)
Science
, vol.312
, pp. 443-446
-
-
Bonacci, T.M.1
Mathews, J.L.2
Yuan, C.3
Lehmann, D.M.4
Malik, S.5
Wu, D.6
Font, J.L.7
Bidlack, J.M.8
Smrcka, A.V.9
-
2
-
-
33845769526
-
-
Submitted for publication
-
Cheng, A. C.; Coleman, R. G.; Smyth, K. T.; Cao, Q.; Soulard, P.; Caffrey, D.; Salzberg, A.; Huang, E. S. Structure-Based Maximal Affinity Model Predicts Small-Molecule Druggability. Submitted for publication.
-
Structure-based Maximal Affinity Model Predicts Small-molecule Druggability
-
-
Cheng, A.C.1
Coleman, R.G.2
Smyth, K.T.3
Cao, Q.4
Soulard, P.5
Caffrey, D.6
Salzberg, A.7
Huang, E.S.8
-
3
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski, R. A. SURFNET: A Program for Visualizing Molecular Surfaces, Cavities, and Intermolecular Interactions. J. Mol. Graphics 1995, 13, 323-330.
-
(1995)
J. Mol. Graphics
, vol.13
, pp. 323-330
-
-
Laskowski, R.A.1
-
4
-
-
0031370977
-
LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
-
Hendlich, M.; Rippmann, F.; Barnickel, G. LIGSITE: Automatic and Efficient Detection of Potential Small Molecule-Binding Sites in Proteins. J. Mol Graphics Modell. 1997, 15, 359-363.
-
(1997)
J. Mol Graphics Modell.
, vol.15
, pp. 359-363
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
-
5
-
-
0032190305
-
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
-
Liang, J.; Edelsbrunner, H.; Fu, P.; Sudhakar, P. V.; Subramaniam, S. Analytical Shape Computation of Macromolecules: I. Molecular Area and Volume through Alpha Shape. Proteins 1998, 33, 1-17.
-
(1998)
Proteins
, vol.33
, pp. 1-17
-
-
Liang, J.1
Edelsbrunner, H.2
Fu, P.3
Sudhakar, P.V.4
Subramaniam, S.5
-
6
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
Brady G. P., Jr; Stouten P. F. Fast Prediction and Visualization of Protein Binding Pockets with PASS. J. Comput.-Aided Mol. Des. 2000, 14, 383-401.
-
(2000)
J. Comput.-aided Mol. Des.
, vol.14
, pp. 383-401
-
-
Brady Jr., G.P.1
Stouten, P.F.2
-
7
-
-
30144442036
-
A method for localizing ligand binding pockets in protein structures
-
Glaser, F.; Morris, R. J.; Najmanovich, R. J.; Laskowski, R. A.; Thornton, J. M. A Method for Localizing Ligand Binding Pockets in Protein Structures. Proteins 2006, 62, 479-488.
-
(2006)
Proteins
, vol.62
, pp. 479-488
-
-
Glaser, F.1
Morris, R.J.2
Najmanovich, R.J.3
Laskowski, R.A.4
Thornton, J.M.5
-
8
-
-
0025916872
-
Functionality maps of binding sites: A multiple copy simultaneous search method
-
Miranker, A.; Karplus, M. Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method. Proteins 1991, 11, 29-34.
-
(1991)
Proteins
, vol.11
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
9
-
-
0042386537
-
Identification of substrate binding sites in enzymes by computational solvent mapping
-
Silberstein, M.; Dennis, S.; Brown, L.; Kortvelyesi, T.; Clodfelter, K.; Vajda, S. Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping. J. Mol. Biol. 2003, 332, 1095-1113.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 1095-1113
-
-
Silberstein, M.1
Dennis, S.2
Brown, L.3
Kortvelyesi, T.4
Clodfelter, K.5
Vajda, S.6
-
10
-
-
18744394070
-
Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
-
Laurie, A. T.; Jackson, R. M. Q-SiteFinder: An Energy-Based Method for the Prediction of Protein-Ligand Binding Sites. Bioinformatics 2005, 21, 1908-16.
-
(2005)
Bioinformatics
, vol.21
, pp. 1908-1916
-
-
Laurie, A.T.1
Jackson, R.M.2
-
11
-
-
0027219536
-
Multiple copy simultaneous search and construction of ligands in binding sites: Application to inhibitors of HIV-1 aspartic proteinase
-
Caflisch, A.; Miranker, A.; Karplus, M. Multiple Copy Simultaneous Search and Construction of Ligands in Binding Sites: Application to Inhibitors of HIV-1 Aspartic Proteinase. J. Med. Chem. 1993, 36, 2142-2167.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 2142-2167
-
-
Caflisch, A.1
Miranker, A.2
Karplus, M.3
-
12
-
-
0026416668
-
Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
-
Sharp, K. A.; Nicholls, A.; Fine, R. F.; Honig, B. Reconciling the Magnitude of the Microscopic and Macroscopic Hydrophobic Effects. Science 1991, 252, 106-109.
-
(1991)
Science
, vol.252
, pp. 106-109
-
-
Sharp, K.A.1
Nicholls, A.2
Fine, R.F.3
Honig, B.4
-
13
-
-
0034677585
-
The mechanism of hydrophobic solvation depends on solute radius
-
Southall, N. T.; Dill, K. A. The Mechanism of Hydrophobic Solvation Depends on Solute Radius. J. Phys. Chem. B 2000, 104, 1326-1331.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 1326-1331
-
-
Southall, N.T.1
Dill, K.A.2
-
14
-
-
0035289779
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Delivery Rev. 2001, 46, 3-26.
-
(2001)
Adv. Drug Delivery Rev.
, vol.46
, pp. 3-26
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
15
-
-
0030914681
-
Polar molecular surface properties predict the intestinal absorption of drugs in humans
-
Palm, K.; Stenberg, P.; Luthman, K.; Artursson, P. Polar Molecular Surface Properties Predict the Intestinal Absorption of Drugs in Humans. Pharm. Res. 1997, 14, 568-571.
-
(1997)
Pharm. Res.
, vol.14
, pp. 568-571
-
-
Palm, K.1
Stenberg, P.2
Luthman, K.3
Artursson, P.4
-
16
-
-
0037030653
-
Molecular properties that influence the oral bioavailability of drug candidates
-
Veber, D. F.; Johnson, S. R.; Cheng, H. Y.; Smith, B. R.; Ward, K. W.; Kopple, K. D. Molecular Properties that Influence the Oral Bioavailability of Drug Candidates. J. Med. Chem. 2002, 45, 2615-2623.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 2615-2623
-
-
Veber, D.F.1
Johnson, S.R.2
Cheng, H.Y.3
Smith, B.R.4
Ward, K.W.5
Kopple, K.D.6
-
17
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
Lockless, S. W.; Ranganathan, R. Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families. Science 1999, 286, 295-299.
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
18
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
Suel, G. M.; Lockless, S. W.; Wall, M. A.; Ranganathan, R. Evolutionarily Conserved Networks of Residues Mediate Allosteric Communication in Proteins. Nat. Struct. Biol. 2003, 10, 59-69.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 59-69
-
-
Suel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
19
-
-
28644438570
-
An intuitive approach to measuring protein surface curvature
-
Coleman, R. C.; Burr, M. A.; Souvaine, D. L.; Cheng, A. C. An Intuitive Approach to Measuring Protein Surface Curvature. Proteins 2005, 61, 1068-1074.
-
(2005)
Proteins
, vol.61
, pp. 1068-1074
-
-
Coleman, R.C.1
Burr, M.A.2
Souvaine, D.L.3
Cheng, A.C.4
-
20
-
-
0037418171
-
The weighted-volume derivative of a space-filling diagram
-
Edelsbrunner, H.; Koehl, P. The Weighted-Volume Derivative of a Space-Filling Diagram. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 2203-2208.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 2203-2208
-
-
Edelsbrunner, H.1
Koehl, P.2
-
21
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson, L.; Eisenberg, D. Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution. Protein Sci. 1992, 1, 227-235.
-
(1992)
Protein Sci.
, vol.1
, pp. 227-235
-
-
Wesson, L.1
Eisenberg, D.2
-
22
-
-
0031022887
-
Additivity principles in biochemistry
-
Dill, K. A. Additivity Principles in Biochemistry. J. Biol. Chem. 1997, 272, 701-704.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 701-704
-
-
Dill, K.A.1
-
23
-
-
0032568655
-
SMART, a simple molecular architecture research tool: Identification of signaling domains
-
Schultz, J.; Milpetz, F.; Bork, P.; Ponting, C. P. SMART, a Simple Molecular Architecture Research Tool: Identification of Signaling Domains. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5857-5864.
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 5857-5864
-
-
Schultz, J.1
Milpetz, F.2
Bork, P.3
Ponting, C.P.4
-
24
-
-
0345864022
-
SMART 4.0: Towards genomic data integration
-
Letunic, I.; Copley, R. R.; Schmidt, S.; Ciccarelli, F. D.; Doerks, T.; Schultz, J.; Ponting, C. P.; Bork, P. SMART 4.0: Towards Genomic Data Integration. Nucleic Acids Res. 2004, 32, D142-4.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Letunic, I.1
Copley, R.R.2
Schmidt, S.3
Ciccarelli, F.D.4
Doerks, T.5
Schultz, J.6
Ponting, C.P.7
Bork, P.8
-
25
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S. R. Profile Hidden Markov Models. Bioinfomatics 1998, 14, 755-763.
-
(1998)
Bioinfomatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
26
-
-
0038154006
-
Three-dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity
-
Huai, Q.; Wang, H.; Sun, Y.; Kim, H. Y.; Liu, Y.; Ke, H. Three-Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity. Structure 2003, 11, 865-873.
-
(2003)
Structure
, vol.11
, pp. 865-873
-
-
Huai, Q.1
Wang, H.2
Sun, Y.3
Kim, H.Y.4
Liu, Y.5
Ke, H.6
-
27
-
-
0041321268
-
Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules
-
Sung, B. J.; Hwang, K. Y.; Jeon, Y. H.; Lee, J. I.; Heo, Y. S.; Kim, J. H.; Moon, J.; Yoon J. M.; Hyun, Y. L.; Kim, E.; Eum, S. J.; Park, S. Y.; Lee, J. O.; Lee, T. G.; Ro, S.; Cho, J. M. Structure of the Catalytic Domain of Human Phosphodiesterase 5 with Bound Drug Molecules. Nature 2003, 425, 98-102.
-
(2003)
Nature
, vol.425
, pp. 98-102
-
-
Sung, B.J.1
Hwang, K.Y.2
Jeon, Y.H.3
Lee, J.I.4
Heo, Y.S.5
Kim, J.H.6
Moon, J.7
Yoon, J.M.8
Hyun, Y.L.9
Kim, E.10
Eum, S.J.11
Park, S.Y.12
Lee, J.O.13
Lee, T.G.14
Ro, S.15
Cho, J.M.16
-
28
-
-
33746629480
-
Phosphodiesterases in the CNS: Targets for drug development
-
Menniti, F. S.; Faraci, W. S.; Schmidt, C. J. Phosphodiesterases in the CNS: Targets for Drug Development. Nat. Rev. Drug Discovery 2006, 5, 660-670.
-
(2006)
Nat. Rev. Drug Discovery
, vol.5
, pp. 660-670
-
-
Menniti, F.S.1
Faraci, W.S.2
Schmidt, C.J.3
-
29
-
-
18344395134
-
Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site
-
Pargellis, C.; Tong, L.; Churchill, L.; Cirillo, P. F.; Gilmore, T.; Graham, A. G.; Grob, P. M.; Hickey, E. R.; Moss, N.; Pav, S.; Regan, J. Inhibition of p38 MAP Kinase by Utilizing a Novel Allosteric Binding Site. Nat. Struct. Biol. 2002, 9, 268-272.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 268-272
-
-
Pargellis, C.1
Tong, L.2
Churchill, L.3
Cirillo, P.F.4
Gilmore, T.5
Graham, A.G.6
Grob, P.M.7
Hickey, E.R.8
Moss, N.9
Pav, S.10
Regan, J.11
-
30
-
-
0030954172
-
A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket
-
Tong, L.; Pav, S.; White, D. M.; Rogers, S.; Crane, K. M.; Cywin, C. L.; Brown, M. L.; Pargellis, C. A. A Highly Specific Inhibitor of Human p38 MAP Kinase Binds in the ATP Pocket. Nat. Struct. Biol. 1997, 4, 311-316.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 311-316
-
-
Tong, L.1
Pav, S.2
White, D.M.3
Rogers, S.4
Crane, K.M.5
Cywin, C.L.6
Brown, M.L.7
Pargellis, C.A.8
-
31
-
-
3343024236
-
Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2
-
Kannan, N.; Neuwald, A. F. Evolutionary Constraints Associated with Functional Specificity of the CMGC Protein Kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2. Protein Sci. 2004, 13, 2059-2077.
-
(2004)
Protein Sci.
, vol.13
, pp. 2059-2077
-
-
Kannan, N.1
Neuwald, A.F.2
-
32
-
-
0344626926
-
Structural basis for the autoinhibition of c-Abl tyrosine kinase
-
Nagar, B.; Hantschel, O.; Young, M. A.; Scheffzek, K.; Veach, D.; Bornmann, W.; Clarkson, B.; Superti-Furga, G.; Kuriyan, J. Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase. Cell 2003, 112, 859-71.
-
(2003)
Cell
, vol.112
, pp. 859-871
-
-
Nagar, B.1
Hantschel, O.2
Young, M.A.3
Scheffzek, K.4
Veach, D.5
Bornmann, W.6
Clarkson, B.7
Superti-Furga, G.8
Kuriyan, J.9
-
33
-
-
33644889108
-
Allosteric inhibitors of Bcr-abl-dependent cell proliferation
-
Adrian, F. J.; Ding, Q.; Sim, T.; Velentza, A.; Sloan, C.; Liu, Y.; Zhang, G.; Hur, W.; Ding, S.; Manley, P.; Mestan, J.; Fabbro, D.; Gray, N. S. Allosteric Inhibitors of Bcr-abl-Dependent Cell Proliferation. Nat. Chem. Biol. 2006 2, 95-102.
-
(2006)
Nat. Chem. Biol.
, vol.2
, pp. 95-102
-
-
Adrian, F.J.1
Ding, Q.2
Sim, T.3
Velentza, A.4
Sloan, C.5
Liu, Y.6
Zhang, G.7
Hur, W.8
Ding, S.9
Manley, P.10
Mestan, J.11
Fabbro, D.12
Gray, N.S.13
-
34
-
-
33845755856
-
Myristoyl binding site in protein kinases. 3D-SIG laptop session abstract
-
Fortaleza, Brazil, August 6-10
-
Milo, M.; Goldblum, A. A. Myristoyl Binding Site in Protein Kinases. 3D-SIG Laptop Session Abstract. Conference on Intelligent Systems for Molecular Biology, Fortaleza, Brazil, August 6-10, 2006.
-
(2006)
Conference on Intelligent Systems for Molecular Biology
-
-
Milo, M.1
Goldblum, A.A.2
-
35
-
-
0013133162
-
A new test set for validating predictions of protein-ligand interaction
-
Nissink, J. W.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. A new test set for validating predictions of protein-ligand interaction. Proteins 2002, 49, 457-471.
-
(2002)
Proteins
, vol.49
, pp. 457-471
-
-
Nissink, J.W.1
Murray, C.2
Hartshorn, M.3
Verdonk, M.L.4
Cole, J.C.5
Taylor, R.6
-
36
-
-
0033954256
-
The protein data bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 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
-
37
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman, D.; Argos, P. Knowledge-based Protein Secondary Structure Assignment. Proteins 1995, 23, 566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
38
-
-
2542529262
-
Pajek - Analysis and visualization of large networks
-
Jünger, M., Mutzel, P., Eds.; Springer, Berlin
-
Batagelj, V.; Mrvar, A. Pajek - Analysis and Visualization of Large Networks. In Graph Drawing Software; Jünger, M., Mutzel, P., Eds.; Springer, Berlin, 2003; pp 77-103.
-
(2003)
Graph Drawing Software
, pp. 77-103
-
-
Batagelj, V.1
Mrvar, A.2
|