-
1
-
-
0036086308
-
Protein-protein interactions: Lessons learned
-
Sharma, S. K.; Ramsey, T. M.; Bair, K. W. Protein-protein interactions: lessons learned. Curr. Med. Chem.: Anti-Cancer Agents 2002, 2, 311-330.
-
(2002)
Curr. Med. Chem.: Anti-Cancer Agents
, vol.2
, pp. 311-330
-
-
Sharma, S.K.1
Ramsey, T.M.2
Bair, K.W.3
-
2
-
-
0037860938
-
Modulation of protein-protein interactions with small organic molecules
-
Berg, T. Modulation of protein-protein interactions with small organic molecules. Angew. Chem., Int. Ed. Engl. 2003, 42, 2462-2481.
-
(2003)
Angew. Chem., Int. Ed. Engl
, vol.42
, pp. 2462-2481
-
-
Berg, T.1
-
3
-
-
22144454687
-
Strategies for targeting protein-protein interactions with synthetic agents
-
Yin, H.; Hamilton, A. D. Strategies for targeting protein-protein interactions with synthetic agents. Angew. Chem., Int. Ed. Engl. 2005, 44, 4130-4163.
-
(2005)
Angew. Chem., Int. Ed. Engl
, vol.44
, pp. 4130-4163
-
-
Yin, H.1
Hamilton, A.D.2
-
4
-
-
0035370483
-
Regulation and function of the p53 tumor suppressor protein
-
Ryan, K. M.; Phillips, A. C.; Vousden, K. H. Regulation and function of the p53 tumor suppressor protein. Curr. Opin. Cell Biol. 2001, 13, 332-337.
-
(2001)
Curr. Opin. Cell Biol
, vol.13
, pp. 332-337
-
-
Ryan, K.M.1
Phillips, A.C.2
Vousden, K.H.3
-
5
-
-
0037329056
-
The p53-Mdm2 module and the ubiquitin system
-
Michael, D.; Oren, M. The p53-Mdm2 module and the ubiquitin system. Semin. Cancer Biol. 2003, 13, 49-58.
-
(2003)
Semin. Cancer Biol
, vol.13
, pp. 49-58
-
-
Michael, D.1
Oren, M.2
-
6
-
-
0025894713
-
p53 mutations in human cancers
-
Hollstein, M.; Sidransky, D.; Vogelstein, B.; Harris, C. C. p53 mutations in human cancers. Science 1991, 253, 49-53.
-
(1991)
Science
, vol.253
, pp. 49-53
-
-
Hollstein, M.1
Sidransky, D.2
Vogelstein, B.3
Harris, C.C.4
-
7
-
-
0038699629
-
The p53-Mdm2 pathway: Targets for the development of new anticancer therapeutics
-
Zheleva, D. I.; Lane, D. P.; Fischer, P. M. The p53-Mdm2 pathway: targets for the development of new anticancer therapeutics. Mini-Rev. Med. Chem. 2003, 3, 257-270.
-
(2003)
Mini-Rev. Med. Chem
, vol.3
, pp. 257-270
-
-
Zheleva, D.I.1
Lane, D.P.2
Fischer, P.M.3
-
8
-
-
9244232878
-
NMR structure of a complex between MDM2 and a small molecule inhibitor
-
Fry, D. C.; Emerson, S. D.; Palme, S.; Vu, B. T.; Liu, C. M.; Podlaski, F. J. NMR structure of a complex between MDM2 and a small molecule inhibitor. J. Biomol. NMR 2004, 30, 163-173.
-
(2004)
J. Biomol. NMR
, vol.30
, pp. 163-173
-
-
Fry, D.C.1
Emerson, S.D.2
Palme, S.3
Vu, B.T.4
Liu, C.M.5
Podlaski, F.J.6
-
9
-
-
10744221485
-
In vivo activation of the p53 pathway by small-molecule antagonists of MDM2
-
Vassilev, L. T.; Vu, B. T.; Graves, B.; Carvajal, D.; Podlaski, F.; Filipovic, Z.; Kong, N.; Kammlott, U.; Lukacs, C.; Klein, C.; Fotouhi, N.; Liu, E. A. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 2004, 303, 844-848.
-
(2004)
Science
, vol.303
, pp. 844-848
-
-
Vassilev, L.T.1
Vu, B.T.2
Graves, B.3
Carvajal, D.4
Podlaski, F.5
Filipovic, Z.6
Kong, N.7
Kammlott, U.8
Lukacs, C.9
Klein, C.10
Fotouhi, N.11
Liu, E.A.12
-
10
-
-
13944274061
-
-
Grasberger, B. L.; Lu, T.; Schubert, C.; Parks, D. J.; Carver, T. E.; Koblish, H. K.; Cummings, M. D.; LaFrance, L. V.; Milkiewicz, K. L.; Calvo, R. R.; Maguire, D.; Lattanze, J.; Franks, C. F.; Zhao, S.; Ramachandren, K.; Bylebyl, G. R.; Zhang, M.; Manthey, C. L.; Petrella, E. C.; Pantoliano, M. W.; Deckman, I. C.; Spurlino, J. C.; Maroney, A. C.; Tomczuk, B. E.; Molloy, C. J.; Bone, R. F. Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells. J. Med. Chem. 2005, 48, 909-912.
-
Grasberger, B. L.; Lu, T.; Schubert, C.; Parks, D. J.; Carver, T. E.; Koblish, H. K.; Cummings, M. D.; LaFrance, L. V.; Milkiewicz, K. L.; Calvo, R. R.; Maguire, D.; Lattanze, J.; Franks, C. F.; Zhao, S.; Ramachandren, K.; Bylebyl, G. R.; Zhang, M.; Manthey, C. L.; Petrella, E. C.; Pantoliano, M. W.; Deckman, I. C.; Spurlino, J. C.; Maroney, A. C.; Tomczuk, B. E.; Molloy, C. J.; Bone, R. F. Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells. J. Med. Chem. 2005, 48, 909-912.
-
-
-
-
11
-
-
3142781225
-
Small-molecule inhibitors of protein-protein interactions: Progressing towards the dream
-
Arkin, M. R.; Wells, J. A. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat. Rev. Drug Discovery 2004, 3, 301-317.
-
(2004)
Nat. Rev. Drug Discovery
, vol.3
, pp. 301-317
-
-
Arkin, M.R.1
Wells, J.A.2
-
12
-
-
0002833057
-
Docking Small ligands in flexible binding sites
-
Apostolakis, J.; Plueckthun, A.; Caflisch, A. Docking Small ligands in flexible binding sites. J. Comput. Chem. 1997, 19, 21-37.
-
(1997)
J. Comput. Chem
, vol.19
, pp. 21-37
-
-
Apostolakis, J.1
Plueckthun, A.2
Caflisch, A.3
-
13
-
-
1542316339
-
Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
-
Zacharias, M. Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP. Proteins 2004, 54, 759-767.
-
(2004)
Proteins
, vol.54
, pp. 759-767
-
-
Zacharias, M.1
-
14
-
-
33750056673
-
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
-
Meiler, J.; Baker, D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 2006, 65, 538-548.
-
(2006)
Proteins
, vol.65
, pp. 538-548
-
-
Meiler, J.1
Baker, D.2
-
15
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa, F. S.; Fernandes, P. A.; Ramos, M. J. Protein-ligand docking: current status and future challenges. Proteins 2006, 65, 15-26.
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, F.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
16
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
Brady, G. P.; Stouten, P. F. W. Fast prediction and visualization of protein binding pockets with PASS. J. Comput.-Aided Mol. Des. 2000, 14, 383-401. http://www.ccl.net/cca/software/UNIX/pass/ overview.shtml.
-
(2000)
J. Comput.-Aided Mol. Des
, vol.14
, pp. 383-401
-
-
Brady, G.P.1
Stouten, P.F.W.2
-
17
-
-
0027053611
-
POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
-
Levitt, D. G.; Banaszak, L. J. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graphics 1992, 10, 229-234.
-
(1992)
J. Mol. Graphics
, vol.10
, pp. 229-234
-
-
Levitt, D.G.1
Banaszak, L.J.2
-
18
-
-
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
-
19
-
-
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
-
20
-
-
18744394070
-
Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
-
Laurie, A. T. R.; Jackson, R. M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21, 1908-1916.
-
(2005)
Bioinformatics
, vol.21
, pp. 1908-1916
-
-
Laurie, A.T.R.1
Jackson, R.M.2
-
21
-
-
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
-
22
-
-
25844478436
-
In-silico screening using flexible ligand binding pockets: A molecular dynamics-based approach
-
Sivanesan, D.; Rajnarayanan, R. V.; Doherty, J.; Pattabiraman, N. In-silico screening using flexible ligand binding pockets: a molecular dynamics-based approach. J. Comput.-Aided Mol. Des. 2005, 19, 213-228.
-
(2005)
J. Comput.-Aided Mol. Des
, vol.19
, pp. 213-228
-
-
Sivanesan, D.1
Rajnarayanan, R.V.2
Doherty, J.3
Pattabiraman, N.4
-
23
-
-
28644443463
-
Molecular docking of balanol to dynamics snapshots of protein kinase A
-
Wong, C. F.; Kua, J.; Zhang, Y.; Straatsma, T. P.; McCammon, J. A. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins 2005, 61, 850-858.
-
(2005)
Proteins
, vol.61
, pp. 850-858
-
-
Wong, C.F.1
Kua, J.2
Zhang, Y.3
Straatsma, T.P.4
McCammon, J.A.5
-
24
-
-
33745880692
-
Computational sampling of a cryptic drug binding site in a protein receptor: Explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase
-
Frembgen-Kesner, T.; Elcock, A. H. Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase. J. Mol. Biol. 2006, 359, 202-214.
-
(2006)
J. Mol. Biol
, vol.359
, pp. 202-214
-
-
Frembgen-Kesner, T.1
Elcock, A.H.2
-
25
-
-
33846417622
-
Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules
-
Helms, V. Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules. ChemPhysChem 2007, 8, 23-33.
-
(2007)
ChemPhysChem
, vol.8
, pp. 23-33
-
-
Helms, V.1
-
26
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662. http://autodock.scripps.edu.
-
(1998)
J. Comput. Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
27
-
-
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. http://www.rcsb.org.
-
(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
-
28
-
-
0037375615
-
Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all atom statistical potential and the AMBER force field with the generalized Born solvation model
-
de Bakker, P. I.; DePristo, M. A.; Burke, D. F.; Blundell, T. L. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all atom statistical potential and the AMBER force field with the generalized Born solvation model. Proteins 2003, 51, 21-40. http://mordred.bioc.cam.ac.uk/~rapper.
-
(2003)
Proteins
, vol.51
, pp. 21-40
-
-
de Bakker, P.I.1
DePristo, M.A.2
Burke, D.F.3
Blundell, T.L.4
-
29
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7, 306-317. www.gromacs.org/.
-
(2001)
J. Mol. Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
30
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236.
-
(1996)
J. Am. Chem. Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
31
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
32
-
-
33846823909
-
Particle mesh ewald: An n log-(n) method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle mesh ewald: An n log-(n) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
33
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684-3690.
-
(1984)
J. Chem. Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
34
-
-
0000388705
-
A linear constraint solver for molecular simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18, 1463-1472.
-
(1997)
J. Comput. Chem
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.4
LINCS, M.5
-
35
-
-
0029878720
-
Visual molecular dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD. Visual molecular dynamics. J. Mol. Graphics 1996, 14, 33-38. http://www.ks.uiuc.edu/ Research/vmd/.
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.V.3
-
36
-
-
0033397980
-
-
Sanner, M. F. Python: a programming language for software integration and development. J. Mol. Graphics Modell. 1999, 17, 57-61. http://mgltools.scripps.edu.
-
Sanner, M. F. Python: a programming language for software integration and development. J. Mol. Graphics Modell. 1999, 17, 57-61. http://mgltools.scripps.edu.
-
-
-
-
37
-
-
49149147973
-
Iterative partial equilibration of orbital electronegativity - a rapid access to atomic charges
-
Gasteiger, J.; Marsili, M. Iterative partial equilibration of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228.
-
(1980)
Tetrahedron
, vol.36
, pp. 3219-3228
-
-
Gasteiger, J.1
Marsili, M.2
|