[ Pobierz całość w formacie PDF ]
108 Buch, I., Giorgino, T. & De Fabritiis, G. 2011 Complete 123 Fiorin, G., Pastore, A., Carloni, P. & Parrinello, M. 2006
reconstruction of an enzyme-inhibitor binding process by Using metadynamics to understand the mechanism of
molecular dynamics simulations. Proc. Natl Acad. Sci. calmodulin/target recognition at atomic detail. Biophys.
USA 108, 10 184 10 189. (doi:10.1073/pnas.1103547108) J. 91, 2768 2777. (doi:10.1529/biophysj.106.086611)
109 Mobley, D. L. & Dill, K. A. 2009 Binding of small- 124 Gervasio, F. L., Laio, A. & Parinello, M. 2005 Flexible
molecule ligands to proteins: what you see is not always docking in solution using metadynamics. J. Am. Chem.
what you get. Structure 17, 489 498. (doi:10.1016/j. Soc. 127, 2600 2607. (doi:10.1021/ja0445950)
str.2009.02.010) 125 Masetti, M., Cavalli, A., Recanatini, M. & Gervasio, F. L.
110 Weis, A., Katebzadeh, K., Söderhjelm, P., Nilsson, I. & 2009 Exploring complex protein ligand recognition mech-
Ryde, U. 2006 Ligand affinities predicted with the anisms with coarse metadynamics. J. Phys. Chem. B 113,
MM/PBSA method: dependence on the simulation 4807 4816. (doi:10.1021/jp803936q)
method and the force field. J. Med. Chem. 49, 6596 126 Swinney, D. C. 2009 The role of binding kinetics in thera-
6606. (doi:10.1021/jm0608210) peutically useful drug action. Curr. Opin. Drug Discov.
111 Wang, J., Morin, P., Wang, W. & Kollman, P. A. 2001 Dev. 12, 31 39.
Use of MM-PBSA in reproducing the binding free ener- 127 Sanchez, C., Lachaize, C., Janody, F., Bellon, B., Röder,
gies to HIV-1 RT of TIBO derivatives and predicting L., Euzenat, J., Rechenmann, F. & Jacq, B. 1999 Grasping
the binding mode to HIV-1 RT of efavirenz by docking at molecular interactions and genetic networks in Droso-
and MM-PBSA. J. Am. Chem. Soc. 123, 5221 5230. phila melanogaster using FlyNets, an Internet database.
(doi:10.1021/ja003834q) Nucleic Acids Res. 27, 89 94. (doi:10.1093/nar/27.1.89)
112 Okimoto, N., Futatsugi, N., Fuji, H., Suenaga, A., Mori- 128 Li, S. et al. 2004 A map of the interactome network of
moto, G., Yanai, R., Ohno, Y., Narumi, T. & Taiji, M. the metazoan C. elegans. Science 303, 540 543. (doi:10.
2009 High performance drug discovery: computational 1126/science.1091403)
screening by combining docking and molecular dynamics 129 Costanzo, M. et al. 2010 The genetic landscape of a cell.
simulations. PLoS Comput. Biol. 5, e1000528. (doi:10. Science 327, 425 431. (doi:10.1126/science.1180823)
1371/journal.pcbi.1000528) 130 Pache, R. A. & Aloy, P. 2008 Incorporating high-
113 Guimaraes, C. R. W. & Cardozo, M. 2008 MM-GB/SA throughput proteomics experiments into structural
rescoring of docking poses in structure-based lead optim- biology pipelines: identification of the low-hanging
ization. J. Chem. Inf. Model. 48, 958 970. (doi:10.1021/ fruits. Proteomics 8, 1959 1964. (doi:10.1002/pmic.
ci800004w) 200700966)
114 Lyne, P. D., Lamb, M. L. & Saeh, J. C. 2006 Accurate 131 Simonis, N. et al. 2009 Empirically controlled mapping of
prediction of the relative potencies of members of a the Caenorhabditis elegans protein protein interactome
series of kinase inhibitors using molecular docking and network. Nat Methods 6, 47 54. (doi:10.1038/nmeth.
MM-GBSA scoring. J. Med. Chem. 49, 4805 4808. 1279)
(doi:10.1021/jm060522a) 132 Reynolds, K. A., Hanes, M. S., Thomson, J. M., Antczak,
115 Moitessier, N., Englebienne, P., Lee, D., Lawandi, J. & A. J., Berger, J. M., Bonomo, R. A., Kirsch, J. F. &
Corbeil, C. R. 2008 Towards the development of univer- Handel, T. M. 2008 Computational redesign of the
sal, fast and highly accurate docking/scoring methods: a SHV-1 b-lactamase/beta-lactamase inhibitor protein
long way to go. Br. J. Pharmacol. 153, S7 S26. interface. J. Mol. Biol. 382, 1265 1275. (doi:10.1016/j.
116 Yang, C. Y., Sun, H., Chen, J., Nikolovska-Coleska, Z. & jmb.2008.05.051)
Wang, S. 2009 Importance of ligand reorganization free 133 Kiel, C., Filchtinski, D., Spoerner, M., Schreiber, G.,
energy in protein ligand binding-affinity prediction. J Kalbitzer, H. R. & Herrmann, C. 2009 Improved binding
Am Chem Soc. 131, 13709 13721. (doi:10.1021/ of raf to Ras.GDP is correlated with biological activity.
ja9039373) J. Biol. Chem. 284, 31893 31902. (doi:10.1074/jbc.
117 Hou, T., Wang, J., Li, Y. & Wang, W. 2011 Assessing the M109.031153)
performance of the MM/PBSA and MM/GBSA 134 Bonvin, A. 2006 Flexible protein protein docking. Curr.
methods. 1. The accuracy of binding free energy calcu- Opin. Struct. Biol. 16, 194 200. (doi:10.1016/j.sbi.2006.
lations based on molecular dynamics simulations. 02.002)
J. Chem. Inf. Model. 51, 69 82. (doi:10.1021/ci100275a) 135 Lensink, M. F., Méndez, R. & Wodak, S. J. 2007 Docking
118 Simonson, T., Archontis, G. & Karplus, M. 2002 Free and scoring protein complexes: CAPRI 3rd edn. Proteins
energy simulations come of age: protein ligand inter- 69, 704 718. (doi:10.1002/prot.21804) [ Pobierz całość w formacie PDF ]
zanotowane.pl doc.pisz.pl pdf.pisz.pl szkicerysunki.xlx.pl
108 Buch, I., Giorgino, T. & De Fabritiis, G. 2011 Complete 123 Fiorin, G., Pastore, A., Carloni, P. & Parrinello, M. 2006
reconstruction of an enzyme-inhibitor binding process by Using metadynamics to understand the mechanism of
molecular dynamics simulations. Proc. Natl Acad. Sci. calmodulin/target recognition at atomic detail. Biophys.
USA 108, 10 184 10 189. (doi:10.1073/pnas.1103547108) J. 91, 2768 2777. (doi:10.1529/biophysj.106.086611)
109 Mobley, D. L. & Dill, K. A. 2009 Binding of small- 124 Gervasio, F. L., Laio, A. & Parinello, M. 2005 Flexible
molecule ligands to proteins: what you see is not always docking in solution using metadynamics. J. Am. Chem.
what you get. Structure 17, 489 498. (doi:10.1016/j. Soc. 127, 2600 2607. (doi:10.1021/ja0445950)
str.2009.02.010) 125 Masetti, M., Cavalli, A., Recanatini, M. & Gervasio, F. L.
110 Weis, A., Katebzadeh, K., Söderhjelm, P., Nilsson, I. & 2009 Exploring complex protein ligand recognition mech-
Ryde, U. 2006 Ligand affinities predicted with the anisms with coarse metadynamics. J. Phys. Chem. B 113,
MM/PBSA method: dependence on the simulation 4807 4816. (doi:10.1021/jp803936q)
method and the force field. J. Med. Chem. 49, 6596 126 Swinney, D. C. 2009 The role of binding kinetics in thera-
6606. (doi:10.1021/jm0608210) peutically useful drug action. Curr. Opin. Drug Discov.
111 Wang, J., Morin, P., Wang, W. & Kollman, P. A. 2001 Dev. 12, 31 39.
Use of MM-PBSA in reproducing the binding free ener- 127 Sanchez, C., Lachaize, C., Janody, F., Bellon, B., Röder,
gies to HIV-1 RT of TIBO derivatives and predicting L., Euzenat, J., Rechenmann, F. & Jacq, B. 1999 Grasping
the binding mode to HIV-1 RT of efavirenz by docking at molecular interactions and genetic networks in Droso-
and MM-PBSA. J. Am. Chem. Soc. 123, 5221 5230. phila melanogaster using FlyNets, an Internet database.
(doi:10.1021/ja003834q) Nucleic Acids Res. 27, 89 94. (doi:10.1093/nar/27.1.89)
112 Okimoto, N., Futatsugi, N., Fuji, H., Suenaga, A., Mori- 128 Li, S. et al. 2004 A map of the interactome network of
moto, G., Yanai, R., Ohno, Y., Narumi, T. & Taiji, M. the metazoan C. elegans. Science 303, 540 543. (doi:10.
2009 High performance drug discovery: computational 1126/science.1091403)
screening by combining docking and molecular dynamics 129 Costanzo, M. et al. 2010 The genetic landscape of a cell.
simulations. PLoS Comput. Biol. 5, e1000528. (doi:10. Science 327, 425 431. (doi:10.1126/science.1180823)
1371/journal.pcbi.1000528) 130 Pache, R. A. & Aloy, P. 2008 Incorporating high-
113 Guimaraes, C. R. W. & Cardozo, M. 2008 MM-GB/SA throughput proteomics experiments into structural
rescoring of docking poses in structure-based lead optim- biology pipelines: identification of the low-hanging
ization. J. Chem. Inf. Model. 48, 958 970. (doi:10.1021/ fruits. Proteomics 8, 1959 1964. (doi:10.1002/pmic.
ci800004w) 200700966)
114 Lyne, P. D., Lamb, M. L. & Saeh, J. C. 2006 Accurate 131 Simonis, N. et al. 2009 Empirically controlled mapping of
prediction of the relative potencies of members of a the Caenorhabditis elegans protein protein interactome
series of kinase inhibitors using molecular docking and network. Nat Methods 6, 47 54. (doi:10.1038/nmeth.
MM-GBSA scoring. J. Med. Chem. 49, 4805 4808. 1279)
(doi:10.1021/jm060522a) 132 Reynolds, K. A., Hanes, M. S., Thomson, J. M., Antczak,
115 Moitessier, N., Englebienne, P., Lee, D., Lawandi, J. & A. J., Berger, J. M., Bonomo, R. A., Kirsch, J. F. &
Corbeil, C. R. 2008 Towards the development of univer- Handel, T. M. 2008 Computational redesign of the
sal, fast and highly accurate docking/scoring methods: a SHV-1 b-lactamase/beta-lactamase inhibitor protein
long way to go. Br. J. Pharmacol. 153, S7 S26. interface. J. Mol. Biol. 382, 1265 1275. (doi:10.1016/j.
116 Yang, C. Y., Sun, H., Chen, J., Nikolovska-Coleska, Z. & jmb.2008.05.051)
Wang, S. 2009 Importance of ligand reorganization free 133 Kiel, C., Filchtinski, D., Spoerner, M., Schreiber, G.,
energy in protein ligand binding-affinity prediction. J Kalbitzer, H. R. & Herrmann, C. 2009 Improved binding
Am Chem Soc. 131, 13709 13721. (doi:10.1021/ of raf to Ras.GDP is correlated with biological activity.
ja9039373) J. Biol. Chem. 284, 31893 31902. (doi:10.1074/jbc.
117 Hou, T., Wang, J., Li, Y. & Wang, W. 2011 Assessing the M109.031153)
performance of the MM/PBSA and MM/GBSA 134 Bonvin, A. 2006 Flexible protein protein docking. Curr.
methods. 1. The accuracy of binding free energy calcu- Opin. Struct. Biol. 16, 194 200. (doi:10.1016/j.sbi.2006.
lations based on molecular dynamics simulations. 02.002)
J. Chem. Inf. Model. 51, 69 82. (doi:10.1021/ci100275a) 135 Lensink, M. F., Méndez, R. & Wodak, S. J. 2007 Docking
118 Simonson, T., Archontis, G. & Karplus, M. 2002 Free and scoring protein complexes: CAPRI 3rd edn. Proteins
energy simulations come of age: protein ligand inter- 69, 704 718. (doi:10.1002/prot.21804) [ Pobierz całość w formacie PDF ]