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Volumn 50, Issue 15, 2007, Pages 3457-3464

Transient pockets on protein surfaces involved in protein-protein interaction

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING PROTEIN; INHIBITOR PROTEIN; INTERLEUKIN 2; PROTEIN; PROTEIN BCL XL; PROTEIN MDM2;

EID: 34547583152     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm070095g     Document Type: Article
Times cited : (204)

References (37)
  • 2
    • 0037860938 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 7
    • 0038699629 scopus 로고    scopus 로고
    • 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
  • 10
    • 13944274061 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 13
    • 1542316339 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 28
    • 0037375615 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 32
    • 33846823909 scopus 로고
    • 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
  • 35
    • 0029878720 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.