-
1
-
-
26444506691
-
Characterization of the 1918 influenza virus polymerase genes
-
Taubenberger, J. K.; Reid, A. H.; Lourens, R. M.; Wang, R.; Jin, G.; Fanning, T. G. Characterization of the 1918 influenza virus polymerase genes. Nature 2005, 437, 889-893.
-
(2005)
Nature
, vol.437
, pp. 889-893
-
-
Taubenberger, J.K.1
Reid, A.H.2
Lourens, R.M.3
Wang, R.4
Jin, G.5
Fanning, T.G.6
-
2
-
-
34447263302
-
Peptide-mediated interference with influenza A virus polymerase
-
Ghanem, A.; Mayer, D.; Chase, G.; Tegge, W.; Frank, R.; Kochs, G.; García-Sastre, A.; Schwemmle, M. Peptide-mediated interference with influenza A virus polymerase. J. Virol. 2007, 81, 7801-7804.
-
(2007)
J. Virol
, vol.81
, pp. 7801-7804
-
-
Ghanem, A.1
Mayer, D.2
Chase, G.3
Tegge, W.4
Frank, R.5
Kochs, G.6
García-Sastre, A.7
Schwemmle, M.8
-
3
-
-
33750267121
-
Role of the influenza virus heterotrimeric RNA polymerase complex in the initiation of replication
-
Deng, T.; Sharps, J. L.; Brownlee, G. G. Role of the influenza virus heterotrimeric RNA polymerase complex in the initiation of replication. J. Gen. Virol. 2006, 87, 3373-3377.
-
(2006)
J. Gen. Virol
, vol.87
, pp. 3373-3377
-
-
Deng, T.1
Sharps, J.L.2
Brownlee, G.G.3
-
4
-
-
0019394947
-
A unique cap (m7GpppXm)- dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription
-
Plotch, S. J.; Bouloy, M.; Ulmanen, I.; Krug, R. M. A unique cap (m7GpppXm)- dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell 1981, 23, 847-858.
-
(1981)
Cell
, vol.23
, pp. 847-858
-
-
Plotch, S.J.1
Bouloy, M.2
Ulmanen, I.3
Krug, R.M.4
-
5
-
-
0029737653
-
Mutational analysis of the influenza virus A/Victoria/3/75 PA protein: Studies of interaction with PB1 protein and identification of a dominant negative mutant
-
Zurcher, T.; de la Luna, S.; Sanz-Ezquerro, J. J.; Nieto, A.; Ortin, J. Mutational analysis of the influenza virus A/Victoria/3/75 PA protein: studies of interaction with PB1 protein and identification of a dominant negative mutant. J. Gen. Virol. 1996, 77, 1745-1749.
-
(1996)
J. Gen. Virol
, vol.77
, pp. 1745-1749
-
-
Zurcher, T.1
de la Luna, S.2
Sanz-Ezquerro, J.J.3
Nieto, A.4
Ortin, J.5
-
6
-
-
0034864841
-
Functional analysis of PA binding by influenza A virus PB1: Effects on polymerase activity and viral infectivity
-
Perez, D. R.; Donis, R. O. Functional analysis of PA binding by influenza A virus PB1: effects on polymerase activity and viral infectivity. J. Virol. 2001, 75, 8127-8136.
-
(2001)
J. Virol
, vol.75
, pp. 8127-8136
-
-
Perez, D.R.1
Donis, R.O.2
-
7
-
-
0036219058
-
Fine mapping of the subunit binding sites of influenza virus RNA polymerase
-
Ohtsu, Y.; Honda, Y.; Sakata, Y.; Kato, H.; Toyoda, T. Fine mapping of the subunit binding sites of influenza virus RNA polymerase. Microbiol. Immunol. 2002, 46, 167-175.
-
(2002)
Microbiol. Immunol
, vol.46
, pp. 167-175
-
-
Ohtsu, Y.1
Honda, Y.2
Sakata, Y.3
Kato, H.4
Toyoda, T.5
-
8
-
-
37349042511
-
Mutational Analyses of Packaging Signals in Influenza Virus PA, PB1,and PB2 Genomic RNA Segments
-
Liang, Y.; Huang, T.; Ly, H.; Parslow, T. G.; Liang, Y. Mutational Analyses of Packaging Signals in Influenza Virus PA, PB1,and PB2 Genomic RNA Segments. J. Virol. 2008, 82, 229-236.
-
(2008)
J. Virol
, vol.82
, pp. 229-236
-
-
Liang, Y.1
Huang, T.2
Ly, H.3
Parslow, T.G.4
Liang, Y.5
-
9
-
-
11144229593
-
Involvement of influenza virus PA subunit in assembly of functional RNA polymerase complexes
-
Kawaguchi, A.; Naito, T.; Nagata, K. Involvement of influenza virus PA subunit in assembly of functional RNA polymerase complexes. J. Virol. 2005, 79, 732-744.
-
(2005)
J. Virol
, vol.79
, pp. 732-744
-
-
Kawaguchi, A.1
Naito, T.2
Nagata, K.3
-
10
-
-
33746815630
-
Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding
-
Hara, K.; Schmidt, F. I.; Crow, M.; Brownlee, G. G. Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding. J. Virol. 2006, 80, 7789-7798.
-
(2006)
J. Virol
, vol.80
, pp. 7789-7798
-
-
Hara, K.1
Schmidt, F.I.2
Crow, M.3
Brownlee, G.G.4
-
11
-
-
0029816205
-
Molecular assembly of the influenza virus RNA polymerase: Determination of the subunit-subunit contact sites
-
Toyoda, T.; Adyshev, D. M.; Kobayashi, M.; Iwata, A.; Ishihama, A. Molecular assembly of the influenza virus RNA polymerase: determination of the subunit-subunit contact sites. J. Gen. Virol. 1996, 77, 2149-2157.
-
(1996)
J. Gen. Virol
, vol.77
, pp. 2149-2157
-
-
Toyoda, T.1
Adyshev, D.M.2
Kobayashi, M.3
Iwata, A.4
Ishihama, A.5
-
12
-
-
0029959077
-
Identification of two separate domains in the influenza virus PB1 protein involved in the interaction with the PB2 and PA subunits: A model for the viral RNA polymerase structure
-
Gonzalez, S.; Zurcher, T.; Ortin, J. Identification of two separate domains in the influenza virus PB1 protein involved in the interaction with the PB2 and PA subunits: a model for the viral RNA polymerase structure. Nucleic Acids Res. 1996, 24, 4456-4463.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4456-4463
-
-
Gonzalez, S.1
Zurcher, T.2
Ortin, J.3
-
13
-
-
67249100913
-
Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site
-
Yuan, P.; Bartlam, M.; Lou, Z.; Chen, S.; Zhou, J.; He, X.; Lv, Z.; Ge, R.; Li, X.; Deng, T.; Fodor, E.; Rao, Z.; Liu, Y. Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site. Nature 2009, 458, 909-914.
-
(2009)
Nature
, vol.458
, pp. 909-914
-
-
Yuan, P.1
Bartlam, M.2
Lou, Z.3
Chen, S.4
Zhou, J.5
He, X.6
Lv, Z.7
Ge, R.8
Li, X.9
Deng, T.10
Fodor, E.11
Rao, Z.12
Liu, Y.13
-
14
-
-
67249130012
-
The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit
-
Dias, A.; Bouvier, D.; Crépin, T.; McCarthy, A. A.; Hart, D.; Baudin, J. F.; Cusack, S.; Ruigrok, R. W. H. The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. Nature 2009, 458, 914-918.
-
(2009)
Nature
, vol.458
, pp. 914-918
-
-
Dias, A.1
Bouvier, D.2
Crépin, T.3
McCarthy, A.A.4
Hart, D.5
Baudin, J.F.6
Cusack, S.7
Ruigrok, R.W.H.8
-
15
-
-
36949001617
-
Strategies of development of antiviral agents directed against influenza virus replication
-
Hsieh, H. P.; Hsu, J. T. Strategies of development of antiviral agents directed against influenza virus replication. Curr. Pharm. Des. 2007, 13, 3531-3542.
-
(2007)
Curr. Pharm. Des
, vol.13
, pp. 3531-3542
-
-
Hsieh, H.P.1
Hsu, J.T.2
-
16
-
-
0019119577
-
A revision of the system of nomenclature for influenza viruses: A WHO memorandum
-
World Health Organization
-
World Health Organization. A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull. W.H.O. 1980, 58, 585-591.
-
(1980)
Bull. W.H.O
, vol.58
, pp. 585-591
-
-
-
17
-
-
0031048319
-
Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: Design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity
-
Kim, C. U.; Lew, W.; Williams, M. A.; Liu, H.; Zhang, L.; Swaminathan, S.; Bischofberger, N.; Chen, M. S.; Mendel, D. B.; Tai, C. Y.; Laver, W. G.; Stevens, R. C. Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: Design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J. Am. Chem. Soc. 1997, 119, 681-690.
-
(1997)
J. Am. Chem. Soc
, vol.119
, pp. 681-690
-
-
Kim, C.U.1
Lew, W.2
Williams, M.A.3
Liu, H.4
Zhang, L.5
Swaminathan, S.6
Bischofberger, N.7
Chen, M.S.8
Mendel, D.B.9
Tai, C.Y.10
Laver, W.G.11
Stevens, R.C.12
-
18
-
-
0027287506
-
Rational design of potent sialidase-based inhibitors of influenza virus replication
-
von Itzstein, M.; Wu, W. Y.; Kok, G. B.; Pegg, M. S.; Dyason, J. C.; Jin, B.; Van Phan, T.; Smythe, M. L.; White, H. F.; Oliver, S. W.; Colman, P. M.; Varghese, J. N.; Ryan, D. M.; Woods, J. M.; Bethell, R. C.; Hotham, V. J.; Cameron, J. M.; Penn, C. R. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 1993, 363, 418-423.
-
(1993)
Nature
, vol.363
, pp. 418-423
-
-
von Itzstein, M.1
Wu, W.Y.2
Kok, G.B.3
Pegg, M.S.4
Dyason, J.C.5
Jin, B.6
Van Phan, T.7
Smythe, M.L.8
White, H.F.9
Oliver, S.W.10
Colman, P.M.11
Varghese, J.N.12
Ryan, D.M.13
Woods, J.M.14
Bethell, R.C.15
Hotham, V.J.16
Cameron, J.M.17
Penn, C.R.18
-
19
-
-
33748437791
-
The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design
-
Russell, R. J.; Haire, L. F.; Stevens, D. J.; Collins, P. J.; Lin, Y. P.; Blackburn, G. Michael.; Hay, A. J.; Gamblin, S. J.; Skehel, J. J. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 2006, 443, 45-49.
-
(2006)
Nature
, vol.443
, pp. 45-49
-
-
Russell, R.J.1
Haire, L.F.2
Stevens, D.J.3
Collins, P.J.4
Lin, Y.P.5
Blackburn6
Michael, G.7
Hay, A.J.8
Gamblin, S.J.9
Skehel, J.J.10
-
20
-
-
36749080401
-
Recent progress in rational drug design of neuraminidase inhibitors
-
Liu, Y.; Zhang, J.; Xu, W. Recent progress in rational drug design of neuraminidase inhibitors. Curr. Med. Chem. 2007, 14, 2872-2891.
-
(2007)
Curr. Med. Chem
, vol.14
, pp. 2872-2891
-
-
Liu, Y.1
Zhang, J.2
Xu, W.3
-
21
-
-
0027185716
-
Ion channel activity of influenza virus M2 protein: Characterization of the amantadine block
-
Wang, C.; Takeuchi, K.; Pinto, L. H.; Lamb, R. A. Ion channel activity of influenza virus M2 protein: characterization of the amantadine block. J. Virol. 1993, 67, 5585-5594.
-
(1993)
J. Virol
, vol.67
, pp. 5585-5594
-
-
Wang, C.1
Takeuchi, K.2
Pinto, L.H.3
Lamb, R.A.4
-
22
-
-
38749151911
-
Structural basis for the function and inhibition of an influenza virus proton channel
-
Stouffer, A. L.; Acharya, R.; Salom, D.; Levine, A. S.; Costanzo, L. D.; Soto, C. S.; Tereshko, V.; Nanda, V.; Stayrook, S.; DeGrado, W. F. Structural basis for the function and inhibition of an influenza virus proton channel. Nature 2008, 451, 596-599.
-
(2008)
Nature
, vol.451
, pp. 596-599
-
-
Stouffer, A.L.1
Acharya, R.2
Salom, D.3
Levine, A.S.4
Costanzo, L.D.5
Soto, C.S.6
Tereshko, V.7
Nanda, V.8
Stayrook, S.9
DeGrado, W.F.10
-
23
-
-
23144440940
-
PRALINE: A multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
-
Simossis, V. A.; Heringa, J. PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 2005, 33, W289-W294.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Simossis, V.A.1
Heringa, J.2
-
24
-
-
50649089174
-
Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus
-
He, X.; Zhou, J.; Bartlam, M.; Zhang, R.; Ma, J.; Lou, Z.; Li, X.; Li, J.; Joachimiak, A.; Zeng, Z.; Ge, R.; Rao, Z.; Liu, Y. Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus. Nature 2008, 454, 1123-1126.
-
(2008)
Nature
, vol.454
, pp. 1123-1126
-
-
He, X.1
Zhou, J.2
Bartlam, M.3
Zhang, R.4
Ma, J.5
Lou, Z.6
Li, X.7
Li, J.8
Joachimiak, A.9
Zeng, Z.10
Ge, R.11
Rao, Z.12
Liu, Y.13
-
25
-
-
50649122962
-
The structural basis for an essential subunit interaction in influenza virus RNA polymerase
-
Obayashi, E.; Yoshida, H.; Kawai, F.; Shibayama, N.; Kawaguchi, A.; Nagata, K.; Tame, J. R. H.; Park, S.-Y. The structural basis for an essential subunit interaction in influenza virus RNA polymerase. Nature 2008, 454, 1127-1131.
-
(2008)
Nature
, vol.454
, pp. 1127-1131
-
-
Obayashi, E.1
Yoshida, H.2
Kawai, F.3
Shibayama, N.4
Kawaguchi, A.5
Nagata, K.6
Tame, J.R.H.7
Park, S.-Y.8
-
26
-
-
0000372879
-
Protein-Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis
-
Stites, W. E. Protein-Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis. Chem. Rev. 1997, 97, 1233-1250.
-
(1997)
Chem. Rev
, vol.97
, pp. 1233-1250
-
-
Stites, W.E.1
-
27
-
-
0347602124
-
Converging Free Energy Estimates: MMPB(GB)SA Studies on the Protein-Protein Complex Ras-Raf
-
Gohlke, H.; Case, D. A. Converging Free Energy Estimates: MMPB(GB)SA Studies on the Protein-Protein Complex Ras-Raf. J. Comput. Chem. 2004, 25, 238-250.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
28
-
-
24344456625
-
Study of the insulin dimerization: Binding free energy calculations and per-residue free energy decomposition
-
Zoete, V.; Meuwly, M.; Karplus, M. Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins: Struct., Funct., Bioinf. 2005, 61, 79-93.
-
(2005)
Proteins: Struct., Funct., Bioinf
, vol.61
, pp. 79-93
-
-
Zoete, V.1
Meuwly, M.2
Karplus, M.3
-
29
-
-
0043245780
-
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
-
Gohlke, H.; Kiel, C.; Case, D. A. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 2003, 330, 891-913.
-
(2003)
J. Mol. Biol
, vol.330
, pp. 891-913
-
-
Gohlke, H.1
Kiel, C.2
Case, D.A.3
-
30
-
-
44149094011
-
Molecular Dynamics-Solvated Interaction Energy Studies of Protein-Protein Interactions: The MP1-p14 Scaffolding Complex
-
Cui, Q.; Sulea, T.; Schrag, J. D.; Munger, C.; Hung, M.-N.; Naïm, M.; Cygler, M.; Purisima, E. O. Molecular Dynamics-Solvated Interaction Energy Studies of Protein-Protein Interactions: The MP1-p14 Scaffolding Complex. J. Mol. Biol. 2008, 379, 787-802.
-
(2008)
J. Mol. Biol
, vol.379
, pp. 787-802
-
-
Cui, Q.1
Sulea, T.2
Schrag, J.D.3
Munger, C.4
Hung, M.-N.5
Naïm, M.6
Cygler, M.7
Purisima, E.O.8
-
31
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 1998, 120, 9401-9409.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
32
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular Molecular mechanics and continuum models
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules: combining molecular 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
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
33
-
-
0242663237
-
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 2003, 24, 1999-2012.
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 2003, 24, 1999-2012.
-
-
-
-
34
-
-
2442480826
-
Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins: Struct., Funct
-
Lee, M. C.; Duan, Y. Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins: Struct., Funct., Bioinform. 2004, 55, 620-634.
-
(2004)
Bioinform
, vol.55
, pp. 620-634
-
-
Lee, M.C.1
Duan, Y.2
-
35
-
-
14244273182
-
Theory and applications of the generalized Born solvation model in macromolecular simulations
-
Tsui, V.; Case, D. A. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 2000, 56, 275-291.
-
(2000)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
36
-
-
20644449471
-
Modification of the generalized Born model suitable for macromolecules
-
Onufriev, A.; Bashford, D.; Case, D. A. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B 2000, 104, 3712-3720.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
37
-
-
3242879771
-
Computational alanine scanning of protein-protein interfaces
-
Kortemme, T.; Kim, D. E.; Baker, D. Computational alanine scanning of protein-protein interfaces. Sci. STKE 2004, 2004, p12.
-
(2004)
Sci. STKE
, vol.2004
, pp. 12
-
-
Kortemme, T.1
Kim, D.E.2
Baker, D.3
-
38
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme, T.; Baker, D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl Acad. Sci. U.S.A. 2002, 99, 14116-14121.
-
(2002)
Proc. Natl Acad. Sci. U.S.A
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
39
-
-
0042710087
-
Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
-
Massova, I.; Kollman, P. A. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 1999, 121, 8133-8143.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
40
-
-
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
-
41
-
-
0031370977
-
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
Barnickel3
LIGSITE, G.4
-
42
-
-
33750029942
-
LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
-
Huang, B.; Schröer, M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 2006, 6, 19-29.
-
(2006)
BMC Struct. Biol
, vol.6
, pp. 19-29
-
-
Huang, B.1
Schröer, M.2
-
43
-
-
38349100452
-
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
-
Brylinski, M.; Skolnick, J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc. Natl Acad. Sci. U.S.A. 2008, 105, 129-134.
-
(2008)
Proc. Natl Acad. Sci. U.S.A
, vol.105
, pp. 129-134
-
-
Brylinski, M.1
Skolnick, J.2
-
44
-
-
34547341277
-
PocketPicker: Analysis of ligand binding-sites with shape descriptors
-
Weisel, M.; Proschak, E.; Schneider, G. PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem. Cent. J. 2007, 1, 1-17.
-
(2007)
Chem. Cent. J
, vol.1
, pp. 1-17
-
-
Weisel, M.1
Proschak, E.2
Schneider, G.3
-
45
-
-
33947420470
-
New method for fast and accurate binding-site identification and analysis
-
Halgren, T. New method for fast and accurate binding-site identification and analysis. Chem. Biol. Drug. Des. 2007, 69, 146-148.
-
(2007)
Chem. Biol. Drug. Des
, vol.69
, pp. 146-148
-
-
Halgren, T.1
-
46
-
-
76249107953
-
-
DeLano Scientific: Palo Alto, CA
-
DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: Palo Alto, CA, 2002. http://www.pymol.org.
-
(2002)
-
-
DeLano, W.L.1
-
47
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26, 1668-1688.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
48
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Struct., Funct., Bioinf. 2006, 65, 712-25.
-
(2006)
Proteins: Struct., Funct., Bioinf
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
49
-
-
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
-
50
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103, 8577-9593.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 8577-9593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
-
51
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
52
-
-
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, 3684-690.
-
(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
-
53
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 1994, 98, 1978-1988.
-
(1994)
J. Phys. Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
54
-
-
28144441347
-
Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
-
Pearlman, D. A. Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J. Med. Chem. 2005, 48, 7796-7807.
-
(2005)
J. Med. Chem
, vol.48
, pp. 7796-7807
-
-
Pearlman, D.A.1
-
55
-
-
39749152456
-
Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases
-
Stoica, I.; Kashif Sadiq, S.; Coveney, P. V. Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases. J. Am. Chem. Soc. 2008, 130, 2639-2648.
-
(2008)
J. Am. Chem. Soc
, vol.130
, pp. 2639-2648
-
-
Stoica, I.1
Kashif Sadiq, S.2
Coveney, P.V.3
-
56
-
-
62649145574
-
Molecular Basis of Inactive B-RAF WT and B-RAF V600E Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study
-
Fratev, F.; Jónsdóttir, S. Ó.; Mihaylova, E.; Pajeva, I. Molecular Basis of Inactive B-RAF WT and B-RAF V600E Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study. Mol. Pharmaceutics 2009, 6, 144-157.
-
(2009)
Mol. Pharmaceutics
, vol.6
, pp. 144-157
-
-
Fratev, F.1
Jónsdóttir, S.O.2
Mihaylova, E.3
Pajeva, I.4
-
57
-
-
0027239578
-
What determines the strength of noncovalent association of ligands to proteins in aqueous solution
-
Miyamoto, S.; Kollman, P. A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402-8406.
-
(1993)
Proc. Natl. Acad. Sci. U.S.A
, vol.90
, pp. 8402-8406
-
-
Miyamoto, S.1
Kollman, P.A.2
-
58
-
-
0034602373
-
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
-
Wang, W.; Kollman, P. A. Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. J. Mol. Biol. 2000, 303, 567-582.
-
(2000)
J. Mol. Biol
, vol.303
, pp. 567-582
-
-
Wang, W.1
Kollman, P.A.2
-
59
-
-
0346996361
-
Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations
-
Masukawa, K. M.; Kollman, P. A.; Kuntz, I. D. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. J. Med. Chem. 2003, 46, 5628-5637.
-
(2003)
J. Med. Chem
, vol.46
, pp. 5628-5637
-
-
Masukawa, K.M.1
Kollman, P.A.2
Kuntz, I.D.3
-
60
-
-
33749511033
-
Thermodynamic Basis for Promiscuity and Selectivity in Protein-Protein Interactions: PDZ Domains, a Case Study
-
Basdevant, N.; Weinstein, H.; Ceruso, M. Thermodynamic Basis for Promiscuity and Selectivity in Protein-Protein Interactions: PDZ Domains, a Case Study. J. Am. Chem. Soc. 2006, 128, 12766-12777.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 12766-12777
-
-
Basdevant, N.1
Weinstein, H.2
Ceruso, M.3
-
61
-
-
84961980685
-
Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
-
Kuhn, B.; Kollman, P. A. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J. Med. Chem. 2000, 43, 3786-3791.
-
(2000)
J. Med. Chem
, vol.43
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
62
-
-
0034811498
-
Use of MMPBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
-
Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MMPBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA. J. Am. Chem. Soc. 2001, 123, 5221-5230.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
63
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995, 8, 127-134.
-
(1995)
Protein Eng
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
64
-
-
0033621044
-
The maximal affinity of ligands
-
Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A. The maximal affinity of ligands. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9997-10002.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A
, vol.96
, pp. 9997-10002
-
-
Kuntz, I.D.1
Chen, K.2
Sharp, K.A.3
Kollman, P.A.4
-
65
-
-
0037079572
-
Free Energy Componenet Analysis of 40 Protein-DNA complexes: A Consensus View on the Thermodynamics of Binding at the Molecular Level
-
Jayaram, B.; McConnell, K.; Dixit, S. B.; Das, A.; Beveridge, D. L. Free Energy Componenet Analysis of 40 Protein-DNA complexes: A Consensus View on the Thermodynamics of Binding at the Molecular Level. J. Comput. Chem. 2002, 23, 1-14.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1-14
-
-
Jayaram, B.1
McConnell, K.2
Dixit, S.B.3
Das, A.4
Beveridge, D.L.5
-
66
-
-
0035160537
-
Barstar is electrostatically optimized for tight binding to barnase
-
Lee, L. P.; Tidor, B. Barstar is electrostatically optimized for tight binding to barnase. Nat. Struct. Biol. 2001, 8, 73-6.
-
(2001)
Nat. Struct. Biol
, vol.8
, pp. 73-76
-
-
Lee, L.P.1
Tidor, B.2
-
67
-
-
0036306236
-
On the Role of Electrostatic Interactions in the Design of Protein-Protein Interfaces
-
Sheinerman, F. B.; Honig, B. On the Role of Electrostatic Interactions in the Design of Protein-Protein Interfaces. J. Mol. Biol. 2002, 318, 161-177.
-
(2002)
J. Mol. Biol
, vol.318
, pp. 161-177
-
-
Sheinerman, F.B.1
Honig, B.2
-
68
-
-
54749087040
-
Mechanism of Fast Peptide Recognition by SH3 Domains
-
Ahmad, M.; Gu, W.; Helms, V. Mechanism of Fast Peptide Recognition by SH3 Domains. Angew. Chem., Int. Ed. 2008, 47, 7626-7630.
-
(2008)
Angew. Chem., Int. Ed
, vol.47
, pp. 7626-7630
-
-
Ahmad, M.1
Gu, W.2
Helms, V.3
|