-
1
-
-
0037422580
-
Flexibilityand molecular recognition in the immune system
-
Jimenez, R.; Salazar, G.; Baldridge, K. K.; Romesberg, F. E. Flexibilityand molecular recognition in the immune system. Proc. Natl.Acad. Sci. USA, 2003, 100, 92-97.
-
(2003)
Proc. Natl.Acad. Sci. USA
, vol.100
, pp. 92-97
-
-
Jimenez, R.1
Salazar, G.2
Baldridge, K.K.3
Romesberg, F.E.4
-
2
-
-
0036420965
-
Molecular recognition in antibody-antigen complexes
-
Sundberg, E. J.; Mariuzza, R. A. Molecular recognition in antibody-antigen complexes. Adv. Protein Chem., 2002, 61, 119-160.
-
(2002)
Adv. Protein Chem.
, vol.61
, pp. 119-160
-
-
Sundberg, E.J.1
Mariuzza, R.A.2
-
4
-
-
0026682657
-
Transcription factors: Structural familiesand principles of DNA recognition
-
Pabo, C. O.; Sauer, R. T. Transcription factors: structural familiesand principles of DNA recognition. Annu. Rev. Biochem., 1992, 61, 1053-1095.
-
(1992)
Annu. Rev. Biochem.
, vol.61
, pp. 1053-1095
-
-
Pabo, C.O.1
Sauer, R.T.2
-
5
-
-
0037008011
-
Multiple conformational changes in enzyme catalysis
-
Hammes, G. G. Multiple conformational changes in enzyme catalysis.Biochemistry, 2002, 41, 8221-8228.
-
(2002)
Biochemistry
, vol.41
, pp. 8221-8228
-
-
Hammes, G.G.1
-
6
-
-
7244258931
-
Quantifying intermolecular interactions: Guidelinesfor the molecular recognition toolbox
-
Hunter, C. A. Quantifying intermolecular interactions: guidelinesfor the molecular recognition toolbox. Angew. Chem. Int. Ed. Engl., 2004, 43, 5310-5324.
-
(2004)
Angew. Chem. Int. Ed. Engl.
, vol.43
, pp. 5310-5324
-
-
Hunter, C.A.1
-
7
-
-
0037008160
-
Approaches to the description and predictionof the binding affinity of small-molecule ligands to macromolecularreceptors
-
Gohlke, H.; Klebe, G. Approaches to the description and predictionof the binding affinity of small-molecule ligands to macromolecularreceptors. Angew. Chem. Int. Ed. Engl., 2002, 41, 2644-2676.
-
(2002)
Angew. Chem. Int. Ed. Engl.
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
8
-
-
0034649618
-
Protein-based virtual screeningof chemical databases. 1. Evaluation of different docking/scoring combinations
-
Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screeningof chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem., 2000, 43, 4759-4767.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 4759-4767
-
-
Bissantz, C.1
Folkers, G.2
Rognan, D.3
-
9
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates fromdocking databases of three-dimensional structures into proteins
-
Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P.Consensus scoring: A method for obtaining improved hit rates fromdocking databases of three-dimensional structures into proteins. J.Med. Chem., 1999, 42, 5100-5109.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
11
-
-
46749144269
-
Scoringfunctions for virtual screening
-
In, Eds.; Bentham Science Publisher
-
Spyrakis, F.; Kellogg, G. E.; Amadasi, A.; Cozzini, P. Scoringfunctions for virtual screening. In Frontiers in Drug Design and Discovery; Eds.; Bentham Science Publisher, 2007, pp 317-379.
-
(2007)
Frontiers in Drug Design and Discovery
, pp. 317-379
-
-
Spyrakis, F.1
Kellogg, G.E.2
Amadasi, A.3
Cozzini, P.4
-
12
-
-
32344449937
-
Docking of aminoglycosidesto hydrated and flexible RNA
-
Moitessier, N.; Westhof, E.; Hanessian, S. Docking of aminoglycosidesto hydrated and flexible RNA. J. Med. Chem., 2006, 49, 1023-1033.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 1023-1033
-
-
Moitessier, N.1
Westhof, E.2
Hanessian, S.3
-
13
-
-
0033674405
-
Virtual screening with solvation and ligand-induced complementarity
-
Schnecke, V.; Kuhn, L. A. Virtual screening with solvation and ligand-induced complementarity. Perspect. Drug Discov. Des., 2000, 20, 171-190.
-
(2000)
Perspect. Drug Discov. Des.
, vol.20
, pp. 171-190
-
-
Schnecke, V.1
Kuhn, L.A.2
-
14
-
-
0031024866
-
Structural correlationsin protein folding funnels
-
Shoemaker, B. A.; Wang, J.; Wolynes, P. G. Structural correlationsin protein folding funnels. Proc. Natl. Acad. Sci. USA, 1997, 94, 777-782.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 777-782
-
-
Shoemaker, B.A.1
Wang, J.2
Wolynes, P.G.3
-
15
-
-
33750014560
-
Solvated docking: Introducingwater into the modelling of biomolecular complexes
-
van Dijk, A. D.; Bonvin, A. M. Solvated docking: introducingwater into the modelling of biomolecular complexes. Bioinformatics, 2006, 22, 2340-2347.
-
(2006)
Bioinformatics
, vol.22
, pp. 2340-2347
-
-
van Dijk, A.D.1
Bonvin, A.M.2
-
16
-
-
26444586139
-
Modelingwater molecules in protein-ligand docking using GOLD
-
Verdonk, M. L.; Chessari, G.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Nissink, J. W.; Taylor, R. D.; Taylor, R. Modelingwater molecules in protein-ligand docking using GOLD. J. Med.Chem., 2005, 48, 6504-6515.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 6504-6515
-
-
Verdonk, M.L.1
Chessari, G.2
Cole, J.C.3
Hartshorn, M.J.4
Murray, C.W.5
Nissink, J.W.6
Taylor, R.D.7
Taylor, R.8
-
17
-
-
0036137713
-
Automated docking to multiple target structures: Incorporationof protein mobility and structural water heterogeneity inAutoDock
-
Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: incorporationof protein mobility and structural water heterogeneity inAutoDock. Proteins, 2002, 46, 34-40.
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
18
-
-
0032961895
-
The particle concept: Placingdiscrete water molecules during protein-ligand docking predictions
-
Rarey, M.; Kramer, B.; Lengauer, T. The particle concept: placingdiscrete water molecules during protein-ligand docking predictions.Proteins, 1999, 34, 17-28.
-
(1999)
Proteins
, vol.34
, pp. 17-28
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
19
-
-
33749021099
-
Development, validation, and application of adapted PEOE charges to estimatepKa values of functional groups in protein-ligand complexes
-
Czodrowski, P.; Dramburg, I.; Sotriffer, C. A.; Klebe, G. Development, validation, and application of adapted PEOE charges to estimatepKa values of functional groups in protein-ligand complexes.Proteins, 2006, 65, 424-437.
-
(2006)
Proteins
, vol.65
, pp. 424-437
-
-
Czodrowski, P.1
Dramburg, I.2
Sotriffer, C.A.3
Klebe, G.4
-
20
-
-
33645060728
-
Probing molecular docking in a charged model binding site
-
Brenk, R.; Vetter, S. W.; Boyce, S. E.; Goodin, D. B.; Shoichet, B.K. Probing molecular docking in a charged model binding site. J.Mol. Biol., 2006, 357, 1449-1470.
-
(2006)
J.Mol. Biol.
, vol.357
, pp. 1449-1470
-
-
Brenk, R.1
Vetter, S.W.2
Boyce, S.E.3
Goodin, D.B.4
Shoichet, B.K.5
-
21
-
-
56449104546
-
Evaluation of different virtual screeningprograms for docking in a charged binding pocket
-
Deng, W.; Verlinde, C. L. Evaluation of different virtual screeningprograms for docking in a charged binding pocket. J. Chem. Inf. Model., 2008, 48, 2010-2020.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 2010-2020
-
-
Deng, W.1
Verlinde, C.L.2
-
22
-
-
36549043024
-
Intrinsic dynamics of enzymesin the unbound state and relation to allosteric regulation
-
Bahar, I.; Chennubhotla, C.; Tobi, D. Intrinsic dynamics of enzymesin the unbound state and relation to allosteric regulation.Curr. Opin. Struct. Biol., 2007, 17, 633-640.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 633-640
-
-
Bahar, I.1
Chennubhotla, C.2
Tobi, D.3
-
23
-
-
0033974667
-
Accommodating protein flexibilityin computational drug design
-
Carlson, H. A.; McCammon, J. A. Accommodating protein flexibilityin computational drug design. Mol. Pharmacol., 2000, 57, 213-218.
-
(2000)
Mol. Pharmacol.
, vol.57
, pp. 213-218
-
-
Carlson, H.A.1
McCammon, J.A.2
-
24
-
-
54549098184
-
Target flexibility: An emerging consideration in drug discovery and design
-
Cozzini, P.; Kellogg, G. E.; Spyrakis, F.; Abraham, D. J.; Costantino, G.; Emerson, A.; Fanelli, F.; Gohlke, H.; Kuhn, L. A.; Morris, G. M.; Orozco, M.; Pertinhez, T. A.; Rizzi, M.; Sotriffer, C. A.Target flexibility: an emerging consideration in drug discovery and design. J. Med. Chem., 2008, 51, 6237-6255.
-
(2008)
J. Med. Chem.
, vol.51
, pp. 6237-6255
-
-
Cozzini, P.1
Kellogg, G.E.2
Spyrakis, F.3
Abraham, D.J.4
Costantino, G.5
Emerson, A.6
Fanelli, F.7
Gohlke, H.8
Kuhn, L.A.9
Morris, G.M.10
Orozco, M.11
Pertinhez, T.A.12
Rizzi, M.13
Sotriffer, C.A.14
-
25
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman, K.; Kern, D. Dynamic personalities of proteins.Nature 2007, 450, 964-972.
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
26
-
-
0033056708
-
Folding funnels, bindingfunnels, and protein function
-
Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R. Folding funnels, bindingfunnels, and protein function. Protein Sci., 1999, 8, 1181-1190.
-
(1999)
Protein Sci.
, vol.8
, pp. 1181-1190
-
-
Tsai, C.J.1
Kumar, S.2
Ma, B.3
Nussinov, R.4
-
27
-
-
55849099561
-
Conformational proofreading: The impact of conformational changes on the specificity of molecular recognition
-
Savir, Y.; Tlusty, T. Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition.PLoS One, 2007, 2, e468.
-
(2007)
PLoS One
, vol.2
-
-
Savir, Y.1
Tlusty, T.2
-
28
-
-
76649114676
-
Protein dynamics and conformational disorder in molecular recognition
-
Mittag, T.; Kay, L. E.; Forman-Kay, J. D. Protein dynamics and conformational disorder in molecular recognition. J. Mol. Recognit., 2010, 23, 105-116.
-
(2010)
J. Mol. Recognit.
, vol.23
, pp. 105-116
-
-
Mittag, T.1
Kay, L.E.2
Forman-Kay, J.D.3
-
29
-
-
0033621118
-
The propagation of binding interactions to remote sites inproteins: Analysis of the binding of the monoclonal antibody D1.3to lysozyme
-
Freire, E. The propagation of binding interactions to remote sites inproteins: analysis of the binding of the monoclonal antibody D1.3to lysozyme. Proc. Natl. Acad. Sci. USA, 1999, 96, 10118-10122.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 10118-10122
-
-
Freire, E.1
-
30
-
-
0032824805
-
Folding funnels and binding mechanisms
-
Ma, B.; Kumar, S.; Tsai, C. J.; Nussinov, R. Folding funnels and binding mechanisms. Protein Eng., 1999, 12, 713-720.
-
(1999)
Protein Eng.
, vol.12
, pp. 713-720
-
-
Ma, B.1
Kumar, S.2
Tsai, C.J.3
Nussinov, R.4
-
31
-
-
0030833567
-
Contacting the protein folding funnel with NMR
-
Onuchic, J. N. Contacting the protein folding funnel with NMR.Proc. Natl. Acad. Sci. USA, 1997, 94, 7129-7131.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 7129-7131
-
-
Onuchic, J.N.1
-
32
-
-
0030435203
-
Protein conformational substates from Xraycrystallography
-
Rejto, P. A.; Freer, S. T. Protein conformational substates from Xraycrystallography. Prog. Biophys. Mol. Biol., 1996, 66, 167-196.
-
(1996)
Prog. Biophys. Mol. Biol.
, vol.66
, pp. 167-196
-
-
Rejto, P.A.1
Freer, S.T.2
-
33
-
-
0001858251
-
Application of a Theory of Enzyme Specificity toProtein Synthesis
-
Koshland, D. E. Application of a Theory of Enzyme Specificity toProtein Synthesis. Proc. Natl. Acad. Sci. USA, 1958, 44, 98-104.
-
(1958)
Proc. Natl. Acad. Sci. USA
, vol.44
, pp. 98-104
-
-
Koshland, D.E.1
-
34
-
-
78651189765
-
On the nature of allosterictransitions: A plausible model
-
Monod, J.; Wyman, J.; Changeux, J. P. On the nature of allosterictransitions: A plausible model. J. Mol. Biol., 1965, 12, 88-118.
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
35
-
-
33845287229
-
Implications of protein conformational diversity for binding and development of new biological active compounds
-
Valente, A. P.; Miyamoto, C. A.; Almeida, F. C. Implications of protein conformational diversity for binding and development of new biological active compounds. Curr. Med. Chem., 2006, 13, 3697-3703.
-
(2006)
Curr. Med. Chem.
, vol.13
, pp. 3697-3703
-
-
Valente, A.P.1
Miyamoto, C.A.2
Almeida, F.C.3
-
36
-
-
0035432947
-
Molecular recognition by induced fit: How fit is theconcept?
-
Bosshard, H. R. Molecular recognition by induced fit: how fit is theconcept? News Physiol. Sci., 2001, 16, 171-173.
-
(2001)
News Physiol. Sci.
, vol.16
, pp. 171-173
-
-
Bosshard, H.R.1
-
37
-
-
0038148710
-
Conformational diversity and proteinevolution-a 60-year-old hypothesis revisited
-
James, L. C.; Tawfik, D. S. Conformational diversity and proteinevolution-a 60-year-old hypothesis revisited. Trends Biochem. Sci., 2003, 28, 361-368.
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 361-368
-
-
James, L.C.1
Tawfik, D.S.2
-
38
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern, D.; Zuiderweg, E. R. The role of dynamics in allosteric regulation.Curr. Opin. Struct. Biol., 2003, 13, 748-757.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.2
-
39
-
-
33645834303
-
New tools provide new insights inNMR studies of protein dynamics
-
Mittermaier, A.; Kay, L. E. New tools provide new insights inNMR studies of protein dynamics. Science, 2006, 312, 224-228.
-
(2006)
Science
, vol.312
, pp. 224-228
-
-
Mittermaier, A.1
Kay, L.E.2
-
40
-
-
34247129655
-
Quantitative molecular ensembleinterpretation of NMR dipolar couplings without restraints
-
Showalter, S. A.; Bruschweiler, R. Quantitative molecular ensembleinterpretation of NMR dipolar couplings without restraints. J.Am. Chem. Soc., 2007, 129, 4158-4159.
-
(2007)
J.Am. Chem. Soc.
, vol.129
, pp. 4158-4159
-
-
Showalter, S.A.1
Bruschweiler, R.2
-
41
-
-
35548976322
-
Open-to-closed transitionin apo maltose-binding protein observed by paramagnetic NMR
-
Tang, C.; Schwieters, C. D.; Clore, G. M. Open-to-closed transitionin apo maltose-binding protein observed by paramagnetic NMR.Nature, 2007, 449, 1078-1082.
-
(2007)
Nature
, vol.449
, pp. 1078-1082
-
-
Tang, C.1
Schwieters, C.D.2
Clore, G.M.3
-
42
-
-
30044434744
-
Structural changes involved in protein bindingcorrelate with intrinsic motions of proteins in the unbound state
-
Tobi, D.; Bahar, I. Structural changes involved in protein bindingcorrelate with intrinsic motions of proteins in the unbound state.Proc. Natl. Acad. Sci. USA, 2005, 102, 18908-18913.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 18908-18913
-
-
Tobi, D.1
Bahar, I.2
-
43
-
-
0028023724
-
Statistical mechanics of kineticproofreading in protein folding in vivo
-
Gulukota, K.; Wolynes, P. G. Statistical mechanics of kineticproofreading in protein folding in vivo. Proc. Natl. Acad. Sci. USA, 1994, 91, 9292-9296.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 9292-9296
-
-
Gulukota, K.1
Wolynes, P.G.2
-
44
-
-
0033970020
-
Folding and binding cascades: Dynamic landscapes and population shifts
-
Kumar, S.; Ma, B.; Tsai, C. J.; Sinha, N.; Nussinov, R. Folding and binding cascades: dynamic landscapes and population shifts. ProteinSci., 2000, 9, 10-19.
-
(2000)
Protein Sci.
, vol.9
, pp. 10-19
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
45
-
-
0033621104
-
Folding and binding cascades: Shifts in energy landscapes
-
Tsai, C. J.; Ma, B.; Nussinov, R. Folding and binding cascades: shifts in energy landscapes. Proc. Natl. Acad. Sci. USA, 1999, 96, 9970-9972.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 9970-9972
-
-
Tsai, C.J.1
Ma, B.2
Nussinov, R.3
-
46
-
-
41649105538
-
Induced-fit or preexisting equilibrium dynamics? Lessons fromprotein crystallography and MD simulations on acetylcholinesteraseand implications for structure-based drug design
-
Xu, Y.; Colletier, J. P.; Jiang, H.; Silman, I.; Sussman, J. L.; Weik, M. Induced-fit or preexisting equilibrium dynamics? Lessons fromprotein crystallography and MD simulations on acetylcholinesteraseand implications for structure-based drug design. ProteinSci., 2008, 17, 601-605.
-
(2008)
ProteinSci.
, vol.17
, pp. 601-605
-
-
Xu, Y.1
Colletier, J.P.2
Jiang, H.3
Silman, I.4
Sussman, J.L.5
Weik, M.6
-
47
-
-
49649084492
-
Dynamic energy landscape view of coupledbinding and protein conformational change: Induced-fit versuspopulation-shift mechanisms
-
Okazaki, K.; Takada, S. Dynamic energy landscape view of coupledbinding and protein conformational change: induced-fit versuspopulation-shift mechanisms. Proc. Natl. Acad. Sci. USA, 2008, 105, 11182-11187.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 11182-11187
-
-
Okazaki, K.1
Takada, S.2
-
48
-
-
52949089027
-
Enzymes with lid-gated active sitesmust operate by an induced fit mechanism instead of conformationalselection
-
Sullivan, S. M.; Holyoak, T. Enzymes with lid-gated active sitesmust operate by an induced fit mechanism instead of conformationalselection. Proc. Natl. Acad. Sci. USA, 2008, 105, 13829-13834.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 13829-13834
-
-
Sullivan, S.M.1
Holyoak, T.2
-
49
-
-
70149090164
-
The intrinsic dynamics of enzymes plays adominant role in determining the structural changes induced uponinhibitor binding
-
Bakan, A.; Bahar, I. The intrinsic dynamics of enzymes plays adominant role in determining the structural changes induced uponinhibitor binding. Proc. Natl. Acad. Sci. USA, 2009, 106, 14349-14354.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 14349-14354
-
-
Bakan, A.1
Bahar, I.2
-
50
-
-
33750337737
-
Protein complex formation by acetylcholinesteraseand the neurotoxin fasciculin-2 appears to involvean induced-fit mechanism
-
Bui, J. M.; McCammon, J. A. Protein complex formation by acetylcholinesteraseand the neurotoxin fasciculin-2 appears to involvean induced-fit mechanism. Proc. Natl. Aca. Sci. USA, 2006, 103, 15451-15456.
-
(2006)
Proc. Natl. Aca. Sci. USA
, vol.103
, pp. 15451-15456
-
-
Bui, J.M.1
McCammon, J.A.2
-
51
-
-
33846625611
-
Fly-casting in protein-DNA binding: Frustration between protein folding and electrostaticsfacilitates target recognition
-
Levy, Y.; Onuchic, J. N.; Wolynes, P. G. Fly-casting in protein-DNA binding: frustration between protein folding and electrostaticsfacilitates target recognition. J. Am. Chem. Soc., 2007, 129, 738-739.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 738-739
-
-
Levy, Y.1
Onuchic, J.N.2
Wolynes, P.G.3
-
52
-
-
34250821717
-
Mechanism of coupledfolding and binding of an intrinsically disordered protein
-
Sugase, K.; Dyson, H. J.; Wright, P. E. Mechanism of coupledfolding and binding of an intrinsically disordered protein. Nature, 2007, 447, 1021-1025.
-
(2007)
Nature
, vol.447
, pp. 1021-1025
-
-
Sugase, K.1
Dyson, H.J.2
Wright, P.E.3
-
53
-
-
36749008588
-
Large-scale allosteric conformationaltransitions of adenylate kinase appear to involve a population-shiftmechanism
-
Arora, K.; Brooks, C. L., 3rd. Large-scale allosteric conformationaltransitions of adenylate kinase appear to involve a population-shiftmechanism. Proc. Natl. Acad. Sci. USA, 2007, 104, 18496-18501.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 18496-18501
-
-
Arora, K.1
Brooks III, C.L.2
-
54
-
-
36749083505
-
Illuminating the mechanistic rolesof enzyme conformational dynamics
-
Hanson, J. A.; Duderstadt, K.; Watkins, L. P.; Bhattacharyya, S.; Brokaw, J.; Chu, J. W.; Yang, H. Illuminating the mechanistic rolesof enzyme conformational dynamics. Proc. Natl. Acad. Sci. USA, 2007, 104, 18055-18060.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 18055-18060
-
-
Hanson, J.A.1
Duderstadt, K.2
Watkins, L.P.3
Bhattacharyya, S.4
Brokaw, J.5
Chu, J.W.6
Yang, H.7
-
55
-
-
0037470496
-
Antibody multispecificitymediated by conformational diversity
-
James, L. C.; Roversi, P.; Tawfik, D. S. Antibody multispecificitymediated by conformational diversity. Science, 2003, 299, 1362-1367.
-
(2003)
Science
, vol.299
, pp. 1362-1367
-
-
James, L.C.1
Roversi, P.2
Tawfik, D.S.3
-
56
-
-
0035957528
-
FlexE: Efficientmolecular docking considering protein structure variations
-
Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: efficientmolecular docking considering protein structure variations. J. Mol.Biol., 2001, 308, 377-395.
-
(2001)
J. Mol.Biol.
, vol.308
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
57
-
-
33947716119
-
A semiempirical freeenergy force field with charge-based desolvation
-
Huey, R.; Morris, G.; Olson, A.; Goodsell, D. A semiempirical freeenergy force field with charge-based desolvation. J. Comput.Chem., 2007, 28, 1145-1152.
-
(2007)
J. Comput.Chem.
, vol.28
, pp. 1145-1152
-
-
Huey, R.1
Morris, G.2
Olson, A.3
Goodsell, D.4
-
58
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Taylor, R. D. Improved protein-ligand docking using GOLD. Proteins, 2003, 52, 609-623.
-
(2003)
Proteins
, vol.52
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
59
-
-
15244353539
-
Side-chain flexibility in proteinligandbinding: The minimal rotation hypothesis
-
Zavodszky, M. I.; Kuhn, L. A. Side-chain flexibility in proteinligandbinding: the minimal rotation hypothesis. Protein Sci., 2005, 14, 1104-1114.
-
(2005)
Protein Sci.
, vol.14
, pp. 1104-1114
-
-
Zavodszky, M.I.1
Kuhn, L.A.2
-
60
-
-
0346264740
-
Automated docking of ligands to an artificialactive site: Augmenting crystallographic analysis with computermodeling
-
Rosenfeld, R. J.; Goodsell, D. S.; Musah, R. A.; Morris, G. M.; Goodin, D. B.; Olson, A. J. Automated docking of ligands to an artificialactive site: augmenting crystallographic analysis with computermodeling. J. Comput. Aided Mol. Des., 2003, 17, 525-536.
-
(2003)
J. Comput. Aided Mol. Des.
, vol.17
, pp. 525-536
-
-
Rosenfeld, R.J.1
Goodsell, D.S.2
Musah, R.A.3
Morris, G.M.4
Goodin, D.B.5
Olson, A.J.6
-
61
-
-
0001147249
-
Harmonic modes as variables to approximatelyaccount for receptor flexibility in ligand-receptordocking simulations: Applications to DNA minor groove ligandcomplex
-
Zacharias, M.; Sklenar, H. Harmonic modes as variables to approximatelyaccount for receptor flexibility in ligand-receptordocking simulations: applications to DNA minor groove ligandcomplex. J. Comput. Chem., 1999, 20, 287-300.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 287-300
-
-
Zacharias, M.1
Sklenar, H.2
-
62
-
-
4544310320
-
Modeling correlated main-chain motions in proteins for flexiblemolecular recognition
-
Zavodszky, M. I.; Lei, M.; Thorpe, M. F.; Day, A. R.; Kuhn, L. A.Modeling correlated main-chain motions in proteins for flexiblemolecular recognition. Proteins, 2004, 57, 243-261.
-
(2004)
Proteins
, vol.57
, pp. 243-261
-
-
Zavodszky, M.I.1
Lei, M.2
Thorpe, M.F.3
Day, A.R.4
Kuhn, L.A.5
-
63
-
-
1442351132
-
Protein flexibility in ligand dockingand virtual screening to protein kinases
-
Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand dockingand virtual screening to protein kinases. J. Mol. Biol., 2004, 337, 209-225.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
64
-
-
21644473891
-
Representingreceptor flexibility in ligand docking through relevant normalmodes
-
Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Representingreceptor flexibility in ligand docking through relevant normalmodes. J. Am. Chem. Soc., 2005, 127, 9632-9640.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
65
-
-
0037424605
-
Efficient conformational sampling of local side-chain flexibility
-
Kallblad, P.; Dean, P. M. Efficient conformational sampling of local side-chain flexibility. J. Mol. Biol., 2003, 326, 1651-1665.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1651-1665
-
-
Kallblad, P.1
Dean, P.M.2
-
66
-
-
37349085453
-
A flexible approach toinduced fit docking
-
Nabuurs, S. B.; Wagener, M.; de Vlieg, J. A flexible approach toinduced fit docking. J. Med. Chem., 2007, 50, 6507-6518.
-
(2007)
J. Med. Chem.
, vol.50
, pp. 6507-6518
-
-
Nabuurs, S.B.1
Wagener, M.2
de Vlieg, J.3
-
67
-
-
41949132916
-
Flexible ligand docking to multiple receptorconformations: A practical alternative
-
Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptorconformations: a practical alternative. Curr. Opin. Struct. Biol., 2008, 18, 178-184.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
68
-
-
34249884544
-
Flexible relaxation of rigidbodydocking solutions
-
Krol, M.; Tournier, A. L.; Bates, P. A. Flexible relaxation of rigidbodydocking solutions. Proteins, 2007, 68, 159-169.
-
(2007)
Proteins
, vol.68
, pp. 159-169
-
-
Krol, M.1
Tournier, A.L.2
Bates, P.A.3
-
69
-
-
21244479779
-
Unveiling the full potential of flexiblereceptor docking using multiple crystallographic structures
-
Barril, X.; Morley, S. D. Unveiling the full potential of flexiblereceptor docking using multiple crystallographic structures. J. Med.Chem., 2005, 48, 4432-4443.
-
(2005)
J. Med.Chem.
, vol.48
, pp. 4432-4443
-
-
Barril, X.1
Morley, S.D.2
-
70
-
-
77951992987
-
Ensemble docking into multiplecrystallographically-derived protein structures: An evaluation basedon the statistical analysis of enrichments
-
Craig, I.; Essex, J.; Spiegel, K. Ensemble docking into multiplecrystallographically-derived protein structures: an evaluation basedon the statistical analysis of enrichments. J. Chem. Inf. Model., 2010, 50, 511-524.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 511-524
-
-
Craig, I.1
Essex, J.2
Spiegel, K.3
-
71
-
-
0036967268
-
Intramoleculardynamics of low molecular weight protein tyrosine phosphatase inmonomer-dimer equilibrium studied by NMR: A model for changesin dynamics upon target binding
-
Akerud, T.; Thulin, E.; Van Etten, R. L.; Akke, M. Intramoleculardynamics of low molecular weight protein tyrosine phosphatase inmonomer-dimer equilibrium studied by NMR: a model for changesin dynamics upon target binding. J. Mol. Biol., 2002, 322, 137-152.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 137-152
-
-
Akerud, T.1
Thulin, E.2
Van Etten, R.L.3
Akke, M.4
-
72
-
-
0036785613
-
Structure and dynamics of copper-free SOD: The protein beforebinding copper
-
Banci, L.; Bertini, I.; Cantini, F.; D'Onofrio, M.; Viezzoli, M. S.Structure and dynamics of copper-free SOD: The protein beforebinding copper. Protein Sci., 2002, 11, 2479-2492.
-
(2002)
Protein Sci.
, vol.11
, pp. 2479-2492
-
-
Banci, L.1
Bertini, I.2
Cantini, F.3
D'Onofrio, M.4
Viezzoli, M.S.5
-
73
-
-
12244298881
-
NMR detection of multiple transitions to low-populated states inazurin
-
Korzhnev, D. M.; Karlsson, B. G.; Orekhov, V. Y.; Billeter, M.NMR detection of multiple transitions to low-populated states inazurin. Protein Sci., 2003, 12, 56-65.
-
(2003)
Protein Sci.
, vol.12
, pp. 56-65
-
-
Korzhnev, D.M.1
Karlsson, B.G.2
Orekhov, V.Y.3
Billeter, M.4
-
74
-
-
0025778840
-
Atomic structure of acetylcholinesterase fromTorpedo californica: A prototypic acetylcholine-binding protein
-
Sussman, J. L.; Harel, M.; Frolow, F.; Oefner, C.; Goldman, A.; Toker, L.; Silman, I. Atomic structure of acetylcholinesterase fromTorpedo californica: a prototypic acetylcholine-binding protein.Science, 1991, 253, 872-879.
-
(1991)
Science
, vol.253
, pp. 872-879
-
-
Sussman, J.L.1
Harel, M.2
Frolow, F.3
Oefner, C.4
Goldman, A.5
Toker, L.6
Silman, I.7
-
75
-
-
0031015343
-
Structure of acetylcholinesterase complexed withthe nootropic alkaloid, (-)-huperzine A
-
Raves, M. L.; Harel, M.; Pang, Y. P.; Silman, I.; Kozikowski, A.P.; Sussman, J. L. Structure of acetylcholinesterase complexed withthe nootropic alkaloid, (-)-huperzine A. Nat. Struct. Biol., 1997, 4, 57-63.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 57-63
-
-
Raves, M.L.1
Harel, M.2
Pang, Y.P.3
Silman, I.4
Kozikowski, A.P.5
Sussman, J.L.6
-
76
-
-
0036480510
-
Rational designof reversible acetylcholinesterase inhibitors
-
Barril, X.; Kalko, S. G.; Orozco, M.; Luque, F. J. Rational designof reversible acetylcholinesterase inhibitors. Mini Rev. Med. Chem., 2002, 2, 27-36.
-
(2002)
Mini Rev. Med. Chem.
, vol.2
, pp. 27-36
-
-
Barril, X.1
Kalko, S.G.2
Orozco, M.3
Luque, F.J.4
-
77
-
-
55249106710
-
Acetylcholinesterase inhibitors as diseasemodifyingtherapies for Alzheimer's disease
-
Muñoz-Torrero, D. Acetylcholinesterase inhibitors as diseasemodifyingtherapies for Alzheimer's disease. Curr. Med. Chem., 2008, 15, 2433-2455.
-
(2008)
Curr. Med. Chem.
, vol.15
, pp. 2433-2455
-
-
Muñoz-Torrero, D.1
-
78
-
-
0027368530
-
Quaternaryligand binding to aromatic residues in the active-site gorge of acetylcholinesterase
-
Harel, M.; Schalk, I.; Ehret-Sabatier, L.; Bouet, F.; Goeldner, M.; Hirth, C.; Axelsen, P. H.; Silman, I.; Sussman, J. L. Quaternaryligand binding to aromatic residues in the active-site gorge of acetylcholinesterase.Proc. Natl. Acad. Sci. USA, 1993, 90, 9031-9035.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 9031-9035
-
-
Harel, M.1
Schalk, I.2
Ehret-Sabatier, L.3
Bouet, F.4
Goeldner, M.5
Hirth, C.6
Axelsen, P.H.7
Silman, I.8
Sussman, J.L.9
-
79
-
-
0037022789
-
3D structure of Torpedo californica acetylcholinesterasecomplexed with huprine X at 2.1 A resolution: Kineticand molecular dynamic correlates
-
Dvir, H.; Wong, D. M.; Harel, M.; Barril, X.; Orozco, M.; Luque, F. J.; Munoz-Torrero, D.; Camps, P.; Rosenberry, T. L.; Silman, I.; Sussman, J. L. 3D structure of Torpedo californica acetylcholinesterasecomplexed with huprine X at 2.1 A resolution: kineticand molecular dynamic correlates. Biochemistry, 2002, 41, 2970-2981.
-
(2002)
Biochemistry
, vol.41
, pp. 2970-2981
-
-
Dvir, H.1
Wong, D.M.2
Harel, M.3
Barril, X.4
Orozco, M.5
Luque, F.J.6
Munoz-Torrero, D.7
Camps, P.8
Rosenberry, T.L.9
Silman, I.10
Sussman, J.L.11
-
80
-
-
0033103478
-
Structure of acetylcholinesterasecomplexed with E2020 (Aricept): Implications for thedesign of new anti-Alzheimer drugs
-
Kryger, G.; Silman, I.; Sussman, J. L. Structure of acetylcholinesterasecomplexed with E2020 (Aricept): implications for thedesign of new anti-Alzheimer drugs. Structure, 1999, 7, 297-307.
-
(1999)
Structure
, vol.7
, pp. 297-307
-
-
Kryger, G.1
Silman, I.2
Sussman, J.L.3
-
81
-
-
0037413712
-
Structural insightsinto ligand interactions at the acetylcholinesterase peripheral anionicsite
-
Bourne, Y.; Taylor, P.; Radic, Z.; Marchot, P. Structural insightsinto ligand interactions at the acetylcholinesterase peripheral anionicsite. EMBO J., 2003, 22, 1-12.
-
(2003)
EMBO J.
, vol.22
, pp. 1-12
-
-
Bourne, Y.1
Taylor, P.2
Radic, Z.3
Marchot, P.4
-
82
-
-
1242342257
-
Freeze-frame inhibitor captures acetylcholinesterase ina unique conformation
-
Bourne, Y.; Kolb, H. C.; Radic, Z.; Sharpless, K. B.; Taylor, P.; Marchot, P. Freeze-frame inhibitor captures acetylcholinesterase ina unique conformation. Proc. Natl. Acad. Sci. USA, 2004, 101, 1449-1454.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 1449-1454
-
-
Bourne, Y.1
Kolb, H.C.2
Radic, Z.3
Sharpless, K.B.4
Taylor, P.5
Marchot, P.6
-
83
-
-
33646063571
-
Conformational flexibility in the peripheralsite of Torpedo californica acetylcholinesterase revealedby the complex structure with a bifunctional inhibitor
-
Colletier, J. P.; Sanson, B.; Nachon, F.; Gabellieri, E.; Fattorusso, C.; Campiani, G.; Weik, M. Conformational flexibility in the peripheralsite of Torpedo californica acetylcholinesterase revealedby the complex structure with a bifunctional inhibitor. J. Am.Chem. Soc., 2006, 128, 4526-4527.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 4526-4527
-
-
Colletier, J.P.1
Sanson, B.2
Nachon, F.3
Gabellieri, E.4
Fattorusso, C.5
Campiani, G.6
Weik, M.7
-
84
-
-
23744474232
-
Crystal packing mediates enantioselectiveligand recognition at the peripheral site of acetylcholinesterase
-
Haviv, H.; Wong, D. M.; Greenblatt, H. M.; Carlier, P. R.; Pang, Y.P.; Silman, I.; Sussman, J. L. Crystal packing mediates enantioselectiveligand recognition at the peripheral site of acetylcholinesterase.J. Am. Chem. Soc., 2005, 127, 11029-11036.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 11029-11036
-
-
Haviv, H.1
Wong, D.M.2
Greenblatt, H.M.3
Carlier, P.R.4
Pang, Y.P.5
Silman, I.6
Sussman, J.L.7
-
85
-
-
33748544640
-
Complexes of alkylene-linked tacrine dimers withTorpedo californica acetylcholinesterase: Binding of Bis5-tacrineproduces a dramatic rearrangement in the active-site gorge
-
Rydberg, E. H.; Brumshtein, B.; Greenblatt, H. M.; Wong, D. M.; Shaya, D.; Williams, L. D.; Carlier, P. R.; Pang, Y. P.; Silman, I.; Sussman, J. L. Complexes of alkylene-linked tacrine dimers withTorpedo californica acetylcholinesterase: Binding of Bis5-tacrineproduces a dramatic rearrangement in the active-site gorge. J. Med.Chem., 2006, 49, 5491-5500.
-
(2006)
J. Med.Chem.
, vol.49
, pp. 5491-5500
-
-
Rydberg, E.H.1
Brumshtein, B.2
Greenblatt, H.M.3
Wong, D.M.4
Shaya, D.5
Williams, L.D.6
Carlier, P.R.7
Pang, Y.P.8
Silman, I.9
Sussman, J.L.10
-
86
-
-
12944255678
-
Structures of recombinant native and E202Q mutanthuman acetylcholinesterase complexed with the snake-venom toxinfasciculin-II
-
Kryger, G.; Harel, M.; Giles, K.; Toker, L.; Velan, B.; Lazar, A.; Kronman, C.; Barak, D.; Ariel, N.; Shafferman, A.; Silman, I.; Sussman, J. L. Structures of recombinant native and E202Q mutanthuman acetylcholinesterase complexed with the snake-venom toxinfasciculin-II. Acta Crystallogr. D Biol. Crystallogr., 2000, 56, 1385-1394.
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 1385-1394
-
-
Kryger, G.1
Harel, M.2
Giles, K.3
Toker, L.4
Velan, B.5
Lazar, A.6
Kronman, C.7
Barak, D.8
Ariel, N.9
Shafferman, A.10
Silman, I.11
Sussman, J.L.12
-
87
-
-
69949089936
-
Pyrano[3, 2-c]quinoline-6-chlorotacrine hybrids as a novel family of acetylcholinesterase-and beta-amyloid-directed anti-Alzheimer compounds
-
Camps, P.; Formosa, X.; Galdeano, C.; Munoz-Torrero, D.; Ramirez, L.; Gomez, E.; Isambert, N.; Lavilla, R.; Badia, A.; Clos, M.V.; Bartolini, M.; Mancini, F.; Andrisano, V.; Arce, M. P.; Rodriguez-Franco, M. I.; Huertas, O.; Dafni, T.; Luque, F. J. Pyrano[3, 2-c]quinoline-6-chlorotacrine hybrids as a novel family of acetylcholinesterase-and beta-amyloid-directed anti-Alzheimer compounds.J. Med. Chem., 2009, 52, 5365-5379.
-
(2009)
J. Med. Chem.
, vol.52
, pp. 5365-5379
-
-
Camps, P.1
Formosa, X.2
Galdeano, C.3
Munoz-Torrero, D.4
Ramirez, L.5
Gomez, E.6
Isambert, N.7
Lavilla, R.8
Badia, A.9
Clos, M.V.10
Bartolini, M.11
Mancini, F.12
Andrisano, V.13
Arce, M.P.14
Rodriguez-Franco, M.I.15
Huertas, O.16
Dafni, T.17
Luque, F.J.18
-
88
-
-
12344307441
-
Conformational changes observed inenzyme crystal structures upon substrate binding
-
Gutteridge, A.; Thornton, J. Conformational changes observed inenzyme crystal structures upon substrate binding. J. Mol. Biol., 2005, 346, 21-28.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 21-28
-
-
Gutteridge, A.1
Thornton, J.2
-
89
-
-
80051747399
-
Incorporating protein flexibility into dockingand structure-based drug design
-
Barril, X.; Fradera, X. Incorporating protein flexibility into dockingand structure-based drug design. Exp. Opin. Drug Discov., 2006, 1, 335-349.
-
(2006)
Exp. Opin. Drug Discov.
, vol.1
, pp. 335-349
-
-
Barril, X.1
Fradera, X.2
-
90
-
-
0031005361
-
Crystal structure of an Hsp90-geldanamycincomplex: Targeting of a protein chaperone by an antitumor agent
-
Stebbins, C. E.; Russo, A. A.; Schneider, C.; Rosen, N.; Hartl, F.U.; Pavletich, N. P. Crystal structure of an Hsp90-geldanamycincomplex: targeting of a protein chaperone by an antitumor agent.Cell, 1997, 89, 239-250.
-
(1997)
Cell
, vol.89
, pp. 239-250
-
-
Stebbins, C.E.1
Russo, A.A.2
Schneider, C.3
Rosen, N.4
Hartl, F.U.5
Pavletich, N.P.6
-
91
-
-
0035071607
-
A small molecule designed tobind to the adenine nucleotide pocket of Hsp90 causes Her2 degradationand the growth arrest and differentiation of breast cancercells
-
Chiosis, G.; Timaul, M. N.; Lucas, B.; Munster, P. N.; Zheng, F.F.; Sepp-Lorenzino, L.; Rosen, N. A small molecule designed tobind to the adenine nucleotide pocket of Hsp90 causes Her2 degradationand the growth arrest and differentiation of breast cancercells. Chem. Biol., 2001, 8, 289-299.
-
(2001)
Chem. Biol.
, vol.8
, pp. 289-299
-
-
Chiosis, G.1
Timaul, M.N.2
Lucas, B.3
Munster, P.N.4
Zheng, F.F.5
Sepp-Lorenzino, L.6
Rosen, N.7
-
92
-
-
3042637928
-
Structure-activity relationships in purinebasedinhibitor binding to HSP90 isoforms
-
Wright, L.; Barril, X.; Dymock, B.; Sheridan, L.; Surgenor, A.; Beswick, M.; Drysdale, M.; Collier, A.; Massey, A.; Davies, N.; Fink, A.; Fromont, C.; Aherne, W.; Boxall, K.; Sharp, S.; Workman, P.; Hubbard, R. E. Structure-activity relationships in purinebasedinhibitor binding to HSP90 isoforms. Chem. Biol., 2004, 11, 775-785.
-
(2004)
Chem. Biol.
, vol.11
, pp. 775-785
-
-
Wright, L.1
Barril, X.2
Dymock, B.3
Sheridan, L.4
Surgenor, A.5
Beswick, M.6
Drysdale, M.7
Collier, A.8
Massey, A.9
Davies, N.10
Fink, A.11
Fromont, C.12
Aherne, W.13
Boxall, K.14
Sharp, S.15
Workman, P.16
Hubbard, R.E.17
-
93
-
-
33646176246
-
Crystal structure of anHsp90-nucleotide-p23/Sba1 closed chaperone complex
-
Ali, M. M.; Roe, S. M.; Vaughan, C. K.; Meyer, P.; Panaretou, B.; Piper, P. W.; Prodromou, C.; Pearl, L. H. Crystal structure of anHsp90-nucleotide-p23/Sba1 closed chaperone complex. Nature, 2006, 440, 1013-1017.
-
(2006)
Nature
, vol.440
, pp. 1013-1017
-
-
Ali, M.M.1
Roe, S.M.2
Vaughan, C.K.3
Meyer, P.4
Panaretou, B.5
Piper, P.W.6
Prodromou, C.7
Pearl, L.H.8
-
94
-
-
33749985149
-
Oral renin inhibitors
-
Staessen, J. A.; Li, Y.; Richart, T. Oral renin inhibitors. Lancet, 2006, 368, 1449-1456.
-
(2006)
Lancet
, vol.368
, pp. 1449-1456
-
-
Staessen, J.A.1
Li, Y.2
Richart, T.3
-
95
-
-
0033577692
-
Substituted piperidines-highly potent renin inhibitors due to induced fit adaptation of theactive site
-
Vieira, E.; Binggeli, A.; Breu, V.; Bur, D.; Fischli, W.; Guller, R.; Hirth, G.; Marki, H. P.; Muller, M.; Oefner, C.; Scalone, M.; Stadler, H.; Wilhelm, M.; Wostl, W. Substituted piperidines-highly potent renin inhibitors due to induced fit adaptation of theactive site. Bioorg. Med. Chem. Lett., 1999, 9, 1397-1402.
-
(1999)
Bioorg. Med. Chem. Lett.
, vol.9
, pp. 1397-1402
-
-
Vieira, E.1
Binggeli, A.2
Breu, V.3
Bur, D.4
Fischli, W.5
Guller, R.6
Hirth, G.7
Marki, H.P.8
Muller, M.9
Oefner, C.10
Scalone, M.11
Stadler, H.12
Wilhelm, M.13
Wostl, W.14
-
96
-
-
67549146537
-
Design and preparation of potent, nonpeptidic, bioavailable renin inhibitors
-
Bezencon, O.; Bur, D.; Weller, T.; Richard-Bildstein, S.; Remen, L.; Sifferlen, T.; Corminboeuf, O.; Grisostomi, C.; Boss, C.; Prade, L.; Delahaye, S.; Treiber, A.; Strickner, P.; Binkert, C.; Hess, P.; Steiner, B.; Fischli, W. Design and preparation of potent, nonpeptidic, bioavailable renin inhibitors. J. Med. Chem., 2009, 52, 3689-3702.
-
(2009)
J. Med. Chem.
, vol.52
, pp. 3689-3702
-
-
Bezencon, O.1
Bur, D.2
Weller, T.3
Richard-Bildstein, S.4
Remen, L.5
Sifferlen, T.6
Corminboeuf, O.7
Grisostomi, C.8
Boss, C.9
Prade, L.10
Delahaye, S.11
Treiber, A.12
Strickner, P.13
Binkert, C.14
Hess, P.15
Steiner, B.16
Fischli, W.17
-
97
-
-
18344395134
-
Inhibition of p38 MAP kinase by utilizing a novel allostericbinding 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 allostericbinding 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
-
98
-
-
0042020196
-
The kinetics of bindingto p38MAP kinase by analogues of BIRB 796
-
Regan, J.; Pargellis, C.; Cirillo, P. F.; Gilmore, T.; Hickey, E. R.; Peet, G.; Proto, A.; Swinamer, A.; Moss, N. The kinetics of bindingto p38MAP kinase by analogues of BIRB 796. Bioorg. Med. Chem.Lett., 2003, 13, 3101-3104.
-
(2003)
Bioorg. Med. Chem.Lett.
, vol.13
, pp. 3101-3104
-
-
Regan, J.1
Pargellis, C.2
Cirillo, P.F.3
Gilmore, T.4
Hickey, E.R.5
Peet, G.6
Proto, A.7
Swinamer, A.8
Moss, N.9
-
99
-
-
34447548576
-
Ligand efficiency indices for effective drugdiscovery
-
Abad-Zapatero, C. Ligand efficiency indices for effective drugdiscovery. Exp. Opin. Drug Discov., 2007, 2, 469-488.
-
(2007)
Exp. Opin. Drug Discov.
, vol.2
, pp. 469-488
-
-
Abad-Zapatero, C.1
-
100
-
-
3543017313
-
Allosteric inhibition of protein tyrosine phosphatase1B
-
Wiesmann, C.; Barr, K. J.; Kung, J.; Zhu, J.; Erlanson, D. A.; Shen, W.; Fahr, B. J.; Zhong, M.; Taylor, L.; Randal, M.; McDowell, R.S.; Hansen, S. K. Allosteric inhibition of protein tyrosine phosphatase1B. Nat. Struct. Mol. Biol., 2004, 11, 730-737.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 730-737
-
-
Wiesmann, C.1
Barr, K.J.2
Kung, J.3
Zhu, J.4
Erlanson, D.A.5
Shen, W.6
Fahr, B.J.7
Zhong, M.8
Taylor, L.9
Randal, M.10
McDowell, R.S.11
Hansen, S.K.12
-
101
-
-
0029066496
-
Structural basis forphosphotyrosine peptide recognition by protein tyrosine phosphatase1B
-
Jia, Z.; Barford, D.; Flint, A. J.; Tonks, N. K. Structural basis forphosphotyrosine peptide recognition by protein tyrosine phosphatase1B. Science, 1995, 268, 1754-1758.
-
(1995)
Science
, vol.268
, pp. 1754-1758
-
-
Jia, Z.1
Barford, D.2
Flint, A.J.3
Tonks, N.K.4
-
102
-
-
58049206736
-
Targeting inactive enzyme conformation: Aryl diketoacid derivatives as a new class of PTP1B inhibitors
-
Liu, S.; Zeng, L. F.; Wu, L.; Yu, X.; Xue, T.; Gunawan, A. M.; Long, Y. Q.; Zhang, Z. Y. Targeting inactive enzyme conformation: aryl diketoacid derivatives as a new class of PTP1B inhibitors.J. Am. Chem. Soc., 2008, 130, 17075-17084.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 17075-17084
-
-
Liu, S.1
Zeng, L.F.2
Wu, L.3
Yu, X.4
Xue, T.5
Gunawan, A.M.6
Long, Y.Q.7
Zhang, Z.Y.8
-
103
-
-
0032897494
-
An analysis of conformationalchanges on protein-protein association: Implications for predictivedocking
-
Betts, M. J.; Sternberg, M. J. An analysis of conformationalchanges on protein-protein association: implications for predictivedocking. Protein Eng., 1999, 12, 271-283.
-
(1999)
Protein Eng.
, vol.12
, pp. 271-283
-
-
Betts, M.J.1
Sternberg, M.J.2
-
104
-
-
9944263528
-
Searching for new allosteric sites in enzymes
-
Hardy, J. A.; Wells, J. A. Searching for new allosteric sites in enzymes.Curr. Opin. Struct. Biol., 2004, 14, 706-715.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 706-715
-
-
Hardy, J.A.1
Wells, J.A.2
-
106
-
-
33646567148
-
Between a rock and a hard place?
-
Whitty, A.; Kumaravel, G. Between a rock and a hard place? Nat.Chem. Biol., 2006, 2, 112-118.
-
(2006)
Nat.Chem. Biol.
, vol.2
, pp. 112-118
-
-
Whitty, A.1
Kumaravel, G.2
-
107
-
-
0032614825
-
Foldingfunnels and conformational transitions via hinge-bending motions
-
Kumar, S.; Ma, B.; Tsai, C. J.; Wolfson, H.; Nussinov, R. Foldingfunnels and conformational transitions via hinge-bending motions.Cell Biochem. Biophys., 1999, 31, 141-164.
-
(1999)
Cell Biochem. Biophys.
, vol.31
, pp. 141-164
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Wolfson, H.4
Nussinov, R.5
-
108
-
-
0037472114
-
Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrierprotein
-
Li, Q.; Khosla, C.; Puglisi, J. D.; Liu, C. W. Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrierprotein. Biochemistry, 2003, 42, 4648-4657.
-
(2003)
Biochemistry
, vol.42
, pp. 4648-4657
-
-
Li, Q.1
Khosla, C.2
Puglisi, J.D.3
Liu, C.W.4
-
109
-
-
14644394262
-
Microsecond-to-millisecondconformational dynamics demarcate the GluR2 glutamate receptorbound to agonists glutamate, quisqualate, and AMPA
-
Valentine, E. R.; Palmer, A. G., 3rd. Microsecond-to-millisecondconformational dynamics demarcate the GluR2 glutamate receptorbound to agonists glutamate, quisqualate, and AMPA. Biochemistry, 2005, 44, 3410-3417.
-
(2005)
Biochemistry
, vol.44
, pp. 3410-3417
-
-
Valentine, E.R.1
Palmer III, A.G.2
-
110
-
-
24044443897
-
Role of conformational heterogeneityin domain swapping and adapter function of the Cks proteins
-
Seeliger, M. A.; Spichty, M.; Kelly, S. E.; Bycroft, M.; Freund, S.M.; Karplus, M.; Itzhaki, L. S. Role of conformational heterogeneityin domain swapping and adapter function of the Cks proteins. J.Biol. Chem., 2005, 280, 30448-30459.
-
(2005)
J.Biol. Chem.
, vol.280
, pp. 30448-30459
-
-
Seeliger, M.A.1
Spichty, M.2
Kelly, S.E.3
Bycroft, M.4
Freund, S.M.5
Karplus, M.6
Itzhaki, L.S.7
-
111
-
-
0037016021
-
Crystal structure and NMR studies of the apo SH2 domains of ZAP-70: Two bikes ratherthan a tandem
-
Folmer, R. H.; Geschwindner, S.; Xue, Y. Crystal structure and NMR studies of the apo SH2 domains of ZAP-70: two bikes ratherthan a tandem. Biochemistry, 2002, 41, 14176-14184.
-
(2002)
Biochemistry
, vol.41
, pp. 14176-14184
-
-
Folmer, R.H.1
Geschwindner, S.2
Xue, Y.3
-
112
-
-
0037457884
-
Identification of a PU.1-IRF4 protein interaction surfacepredicted by chemical exchange line broadening
-
McKercher, S. R.; Lombardo, C. R.; Bobkov, A.; Jia, X.; Assa-Munt, N. Identification of a PU.1-IRF4 protein interaction surfacepredicted by chemical exchange line broadening. Proc. Natl. Acad.Sci. USA, 2003, 100, 511-516.
-
(2003)
Proc. Natl. Acad.Sci. USA
, vol.100
, pp. 511-516
-
-
McKercher, S.R.1
Lombardo, C.R.2
Bobkov, A.3
Jia, X.4
Assa-Munt, N.5
-
113
-
-
22244474963
-
Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein
-
Venkitaramani, D. V.; Fulton, D. B.; Andreotti, A. H.; Johansen, K.M.; Johansen, J. Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein. ProteinSci., 2005, 14, 1894-1901.
-
(2005)
ProteinSci.
, vol.14
, pp. 1894-1901
-
-
Venkitaramani, D.V.1
Fulton, D.B.2
Andreotti, A.H.3
Johansen, K.M.4
Johansen, J.5
-
114
-
-
4344592803
-
Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters
-
Wang, C.; Karpowich, N.; Hunt, J. F.; Rance, M.; Palmer, A. G.Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J.Mol. Biol., 2004, 342, 525-537.
-
(2004)
J.Mol. Biol.
, vol.342
, pp. 525-537
-
-
Wang, C.1
Karpowich, N.2
Hunt, J.F.3
Rance, M.4
Palmer, A.G.5
-
115
-
-
4344649812
-
CBFbeta allosterically regulates the Runx1 Runt domain via a dynamicconformational equilibrium
-
Yan, J.; Liu, Y.; Lukasik, S. M.; Speck, N. A.; Bushweller, J. H.CBFbeta allosterically regulates the Runx1 Runt domain via a dynamicconformational equilibrium. Nat. Struct. Mol. Biol., 2004, 11, 901-906.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 901-906
-
-
Yan, J.1
Liu, Y.2
Lukasik, S.M.3
Speck, N.A.4
Bushweller, J.H.5
-
116
-
-
4444258777
-
Cterminaldomain of insulin-like growth factor (IGF) binding protein6: Conformational exchange and its correlation with IGF-II binding
-
Yao, S.; Headey, S. J.; Keizer, D. W.; Bach, L. A.; Norton, R. S. Cterminaldomain of insulin-like growth factor (IGF) binding protein6: conformational exchange and its correlation with IGF-II binding.Biochemistry, 2004, 43, 11187-11195.
-
(2004)
Biochemistry
, vol.43
, pp. 11187-11195
-
-
Yao, S.1
Headey, S.J.2
Keizer, D.W.3
Bach, L.A.4
Norton, R.S.5
-
117
-
-
0035834765
-
Conformationalheterogeneity in the C-terminal zinc fingers of humanMTF-1: An NMR and zinc-binding study
-
Giedroc, D. P.; Chen, X.; Pennella, M. A.; LiWang, A. C. Conformationalheterogeneity in the C-terminal zinc fingers of humanMTF-1: an NMR and zinc-binding study. J. Biol. Chem., 2001, 276, 42322-42332.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 42322-42332
-
-
Giedroc, D.P.1
Chen, X.2
Pennella, M.A.3
LiWang, A.C.4
-
118
-
-
0036303949
-
Effects of temperatureon the dynamic behaviour of the HIV-1 nucleocapsidNCp7 and its DNA complex
-
Ramboarina, S.; Srividya, N.; Atkinson, R. A.; Morellet, N.; Roques, B. P.; Lefevre, J. F.; Mely, Y.; Kieffer, B. Effects of temperatureon the dynamic behaviour of the HIV-1 nucleocapsidNCp7 and its DNA complex. J. Mol. Biol., 2002, 316, 611-627.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 611-627
-
-
Ramboarina, S.1
Srividya, N.2
Atkinson, R.A.3
Morellet, N.4
Roques, B.P.5
Lefevre, J.F.6
Mely, Y.7
Kieffer, B.8
-
119
-
-
0034765285
-
Delineationof the allosteric mechanism of a cytidylyltransferase exhibitingnegative cooperativity
-
Stevens, S. Y.; Sanker, S.; Kent, C.; Zuiderweg, E. R. Delineationof the allosteric mechanism of a cytidylyltransferase exhibitingnegative cooperativity. Nat. Struct. Biol., 2001, 8, 947-952.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 947-952
-
-
Stevens, S.Y.1
Sanker, S.2
Kent, C.3
Zuiderweg, E.R.4
-
120
-
-
0037013143
-
The conformational plasticity of proteinkinases
-
Huse, M.; Kuriyan, J. The conformational plasticity of proteinkinases. Cell, 2002, 109, 275-282.
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
121
-
-
62549167040
-
Ligandinducedglobal transitions in the catalytic domain of protein kinaseA
-
Hyeon, C.; Jennings, P. A.; Adams, J. A.; Onuchic, J. N. Ligandinducedglobal transitions in the catalytic domain of protein kinaseA. Proc. Natl. Acad. Sci. USA, 2009, 106, 3023-3028.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 3023-3028
-
-
Hyeon, C.1
Jennings, P.A.2
Adams, J.A.3
Onuchic, J.N.4
-
122
-
-
33746565283
-
Molecular dynamics of apo-adenylate kinase: A principal component analysis
-
Lou, H.; Cukier, R. I. Molecular dynamics of apo-adenylate kinase: a principal component analysis. J. Phys. Chem. B, 2006, 110, 12796-12808.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 12796-12808
-
-
Lou, H.1
Cukier, R.I.2
-
123
-
-
33846847773
-
Conformationaltransitions of adenylate kinase: Switching by cracking
-
Whitford, P. C.; Miyashita, O.; Levy, Y.; Onuchic, J. N. Conformationaltransitions of adenylate kinase: switching by cracking. J.Mol. Biol., 2007, 366, 1661-1671.
-
(2007)
J.Mol. Biol.
, vol.366
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
124
-
-
35348911804
-
On the importance of a funneledenergy landscape for the assembly and regulation of multidomainSrc tyrosine kinases
-
Faraldo-Gomez, J. D.; Roux, B. On the importance of a funneledenergy landscape for the assembly and regulation of multidomainSrc tyrosine kinases. Proc. Natl. Acad. Sci. USA, 2007, 104, 13643-13648.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 13643-13648
-
-
Faraldo-Gomez, J.D.1
Roux, B.2
-
125
-
-
41849097740
-
Src kinase conformational activation: Thermodynamics, pathways, and mechanisms
-
Yang, S.; Roux, B. Src kinase conformational activation: thermodynamics, pathways, and mechanisms. PLoS Comput. Biol., 2008, 4, e1000047.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Yang, S.1
Roux, B.2
-
126
-
-
33646755174
-
A Src-like inactiveconformation in the abl tyrosine kinase domain
-
Levinson, N. M.; Kuchment, O.; Shen, K.; Young, M. A.; Koldobskiy, M.; Karplus, M.; Cole, P. A.; Kuriyan, J. A Src-like inactiveconformation in the abl tyrosine kinase domain. PLoS Biol., 2006, 4, e144.
-
(2006)
PLoS Biol.
, vol.4
-
-
Levinson, N.M.1
Kuchment, O.2
Shen, K.3
Young, M.A.4
Koldobskiy, M.5
Karplus, M.6
Cole, P.A.7
Kuriyan, J.8
-
127
-
-
62549151081
-
Protein conformational transitions: Theclosure mechanism of a kinase explored by atomistic simulations
-
Berteotti, A.; Cavalli, A.; Branduardi, D.; Gervasio, F. L.; Recanatini, M.; Parrinello, M. Protein conformational transitions: theclosure mechanism of a kinase explored by atomistic simulations.J. Am. Chem. Soc., 2009, 131, 244-250.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 244-250
-
-
Berteotti, A.1
Cavalli, A.2
Branduardi, D.3
Gervasio, F.L.4
Recanatini, M.5
Parrinello, M.6
-
128
-
-
0035413608
-
Dynamics of cAMP-dependent protein kinase
-
Johnson, D. A.; Akamine, P.; Radzio-Andzelm, E.; Madhusudan, M.; Taylor, S. S. Dynamics of cAMP-dependent protein kinase.Chem. Rev., 2001, 101, 2243-2270.
-
(2001)
Chem. Rev.
, vol.101
, pp. 2243-2270
-
-
Johnson, D.A.1
Akamine, P.2
Radzio-Andzelm, E.3
Madhusudan, M.4
Taylor, S.S.5
-
129
-
-
0000915668
-
2.0 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexedwith a peptide inhibitor and detergent
-
Knighton, D. R.; Bell, S. M.; Zheng, J.; Ten Eyck, L. F.; Xuong, N.H.; Taylor, S. S.; Sowadski, J. M. 2.0 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexedwith a peptide inhibitor and detergent. Acta Cryst. D Biol. Cryst., 1993, 49, 357-361.
-
(1993)
Acta Cryst. D Biol. Cryst.
, vol.49
, pp. 357-361
-
-
Knighton, D.R.1
Bell, S.M.2
Zheng, J.3
Ten Eyck, L.F.4
Xuong, N.H.5
Taylor, S.S.6
Sowadski, J.M.7
-
130
-
-
0027429591
-
Crystal structures of the myristylated catalyticsubunit of cAMP-dependent protein kinase reveal open and closed conformations
-
Zheng, J.; Knighton, D. R.; Xuong, N. H.; Taylor, S. S.; Sowadski, J. M.; Ten Eyck, L. F. Crystal structures of the myristylated catalyticsubunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Sci., 1993, 2, 1559-1573.
-
(1993)
Protein Sci.
, vol.2
, pp. 1559-1573
-
-
Zheng, J.1
Knighton, D.R.2
Xuong, N.H.3
Taylor, S.S.4
Sowadski, J.M.5
Ten Eyck, L.F.6
-
131
-
-
0242268469
-
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitionsin proteins
-
Miyashita, O.; Onuchic, J. N.; Wolynes, P. G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitionsin proteins. Proc. Natl. Acad. Sci. USA, 2003, 100, 12570-12575.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12570-12575
-
-
Miyashita, O.1
Onuchic, J.N.2
Wolynes, P.G.3
-
132
-
-
17644435744
-
Nucleoside monophosphate kinases: Structure, mechanism, and substrate specificity
-
Yan, H.; Tsai, M. D. Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity. Adv. Enzymol. Relat. AreasMol. Biol., 1999, 73, 103-134.
-
(1999)
Adv. Enzymol. Relat. AreasMol. Biol.
, vol.73
, pp. 103-134
-
-
Yan, H.1
Tsai, M.D.2
-
133
-
-
60549089572
-
Inherent flexibility determines the transitionmechanisms of the EF-hands of calmodulin
-
Tripathi, S.; Portman, J. J. Inherent flexibility determines the transitionmechanisms of the EF-hands of calmodulin. Proc. Natl. Acad.Sci. USA, 2009, 106, 2104-2109.
-
(2009)
Proc. Natl. Acad.Sci. USA
, vol.106
, pp. 2104-2109
-
-
Tripathi, S.1
Portman, J.J.2
-
134
-
-
0027052523
-
Calmodulin structure refined at 1.7 A resolution
-
Chattopadhyaya, R.; Meador, W. E.; Means, A. R.; Quiocho, F. A.Calmodulin structure refined at 1.7 A resolution. J. Mol. Biol., 1992, 228, 1177-1192.
-
(1992)
J. Mol. Biol.
, vol.228
, pp. 1177-1192
-
-
Chattopadhyaya, R.1
Meador, W.E.2
Means, A.R.3
Quiocho, F.A.4
-
135
-
-
0029159794
-
Solution structure of calcium-free calmodulin
-
Kuboniwa, H.; Tjandra, N.; Grzesiek, S.; Ren, H.; Klee, C. B.; Bax, A. Solution structure of calcium-free calmodulin. Nat. Struct. Biol., 1995, 2, 768-776.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 768-776
-
-
Kuboniwa, H.1
Tjandra, N.2
Grzesiek, S.3
Ren, H.4
Klee, C.B.5
Bax, A.6
-
136
-
-
0034753415
-
Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains
-
Chou, J. J.; Li, S.; Klee, C. B.; Bax, A. Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains.Nat. Struct. Biol., 2001, 8, 990-997.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 990-997
-
-
Chou, J.J.1
Li, S.2
Klee, C.B.3
Bax, A.4
-
137
-
-
0033546403
-
Backbone dynamicsand energetics of a calmodulin domain mutant exchanging betweenclosed and open conformations
-
Evenas, J.; Forsen, S.; Malmendal, A.; Akke, M. Backbone dynamicsand energetics of a calmodulin domain mutant exchanging betweenclosed and open conformations. J. Mol. Biol., 1999, 289, 603-617.
-
(1999)
J. Mol. Biol.
, vol.289
, pp. 603-617
-
-
Evenas, J.1
Forsen, S.2
Malmendal, A.3
Akke, M.4
-
138
-
-
0035029050
-
Functionaldynamics of the hydrophobic cleft in the N-domain of calmodulin
-
Vigil, D.; Gallagher, S. C.; Trewhella, J.; Garcia, A. E. Functionaldynamics of the hydrophobic cleft in the N-domain of calmodulin.Biophys. J., 2001, 80, 2082-2092.
-
(2001)
Biophys. J.
, vol.80
, pp. 2082-2092
-
-
Vigil, D.1
Gallagher, S.C.2
Trewhella, J.3
Garcia, A.E.4
-
139
-
-
33847617864
-
Slow conformational dynamics and unfolding of the calmodulin C-terminal domain
-
Chen, Y. G.; Hummer, G. Slow conformational dynamics and unfolding of the calmodulin C-terminal domain. J. Am. Chem. Soc., 2007, 129, 2414-2415.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 2414-2415
-
-
Chen, Y.G.1
Hummer, G.2
-
140
-
-
28044463992
-
Correlated dynamics of consecutive residues reveal transient and cooperative unfolding of secondary structure in proteins
-
Lundstrom, P.; Mulder, F. A.; Akke, M. Correlated dynamics of consecutive residues reveal transient and cooperative unfolding of secondary structure in proteins. Proc. Natl. Acad. Sci. USA, 2005, 102, 16984-16989.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 16984-16989
-
-
Lundstrom, P.1
Mulder, F.A.2
Akke, M.3
-
141
-
-
0026794065
-
Target enzyme recognitionby calmodulin: 2.4 A structure of a calmodulin-peptidecomplex
-
Meador, W. E.; Means, A. R.; Quiocho, F. A. Target enzyme recognitionby calmodulin: 2.4 A structure of a calmodulin-peptidecomplex. Science, 1992, 257, 1251-1255.
-
(1992)
Science
, vol.257
, pp. 1251-1255
-
-
Meador, W.E.1
Means, A.R.2
Quiocho, F.A.3
-
142
-
-
69249158109
-
Novel inhibitorscomplexed with glutamate dehydrogenase: Allosteric regulation bycontrol of protein dynamics
-
Li, M.; Smith, C. J.; Walker, M. T.; Smith, T. J. Novel inhibitorscomplexed with glutamate dehydrogenase: allosteric regulation bycontrol of protein dynamics. J. Biol. Chem., 2009, 284, 22988-23000.
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 22988-23000
-
-
Li, M.1
Smith, C.J.2
Walker, M.T.3
Smith, T.J.4
-
143
-
-
62449307954
-
Visualizing breathing motion of internalcavities in concert with ligand migration in myoglobin
-
Tomita, A.; Sato, T.; Ichiyanagi, K.; Nozawa, S.; Ichikawa, H.; Chollet, M.; Kawai, F.; Park, S. Y.; Tsuduki, T.; Yamato, T.; Koshihara, S. Y.; Adachi, S. Visualizing breathing motion of internalcavities in concert with ligand migration in myoglobin. Proc. Natl.Acad. Sci. USA, 2009, 106, 2612-2616.
-
(2009)
Proc. Natl.Acad. Sci. USA
, vol.106
, pp. 2612-2616
-
-
Tomita, A.1
Sato, T.2
Ichiyanagi, K.3
Nozawa, S.4
Ichikawa, H.5
Chollet, M.6
Kawai, F.7
Park, S.Y.8
Tsuduki, T.9
Yamato, T.10
Koshihara, S.Y.11
Adachi, S.12
-
144
-
-
55649119346
-
Solution NMR structuredetermination of proteins revisited
-
Billeter, M.; Wagner, G.; Wuthrich, K. Solution NMR structuredetermination of proteins revisited. J. Biomol. NMR, 2008, 42, 155-158.
-
(2008)
J. Biomol. NMR
, vol.42
, pp. 155-158
-
-
Billeter, M.1
Wagner, G.2
Wuthrich, K.3
-
145
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
Adcock, S. A.; McCammon, J. A. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev., 2006, 106, 1589-1615.
-
(2006)
Chem. Rev.
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
146
-
-
29744459671
-
Induced fit in mouseacetylcholinesterase upon binding a femtomolar inhibitor: A moleculardynamics study
-
Senapati, S.; Bui, J. M.; McCammon, J. A. Induced fit in mouseacetylcholinesterase upon binding a femtomolar inhibitor: a moleculardynamics study. J. Med. Chem., 2005, 48, 8155-8162.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 8155-8162
-
-
Senapati, S.1
Bui, J.M.2
McCammon, J.A.3
-
147
-
-
28544451677
-
Design, synthesis, and biologicalevaluation of dual binding site acetylcholinesterase inhibitors: New disease-modifying agents for Alzheimer's disease
-
Munoz-Ruiz, P.; Rubio, L.; Garcia-Palomero, E.; Dorronsoro, I.; del Monte-Millan, M.; Valenzuela, R.; Usan, P.; de Austria, C.; Bartolini, M.; Andrisano, V.; Bidon-Chanal, A.; Orozco, M.; Luque, F. J.; Medina, M.; Martinez, A. Design, synthesis, and biologicalevaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer's disease. J.Med. Chem., 2005, 48, 7223-7233.
-
(2005)
J.Med. Chem.
, vol.48
, pp. 7223-7233
-
-
Munoz-Ruiz, P.1
Rubio, L.2
Garcia-Palomero, E.3
Dorronsoro, I.4
del Monte-Millan, M.5
Valenzuela, R.6
Usan, P.7
de Austria, C.8
Bartolini, M.9
Andrisano, V.10
Bidon-Chanal, A.11
Orozco, M.12
Luque, F.J.13
Medina, M.14
Martinez, A.15
-
148
-
-
0037125501
-
Studying enzyme bindingspecificity in acetylcholinesterase using a combined molecular dynamicsand multiple docking approach
-
Kua, J.; Zhang, Y.; McCammon, J. A. Studying enzyme bindingspecificity in acetylcholinesterase using a combined molecular dynamicsand multiple docking approach. J. Am. Chem. Soc., 2002, 124, 8260-8267.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 8260-8267
-
-
Kua, J.1
Zhang, Y.2
McCammon, J.A.3
-
149
-
-
0037157153
-
Computational drug design accommodating receptor flexibility: Therelaxed complex scheme
-
Lin, J. H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A.Computational drug design accommodating receptor flexibility: therelaxed complex scheme. J. Am. Chem. Soc., 2002, 124, 5632-5633.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5632-5633
-
-
Lin, J.H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
150
-
-
0037231646
-
Therelaxed complex method: Accommodating receptor flexibility fordrug design with an improved scoring scheme
-
Lin, J. H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. Therelaxed complex method: Accommodating receptor flexibility fordrug design with an improved scoring scheme. Biopolymers, 2003, 68, 47-62.
-
(2003)
Biopolymers
, vol.68
, pp. 47-62
-
-
Lin, J.H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
151
-
-
33747200808
-
Combining docking and molecular dynamic simulations in drug design
-
Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Combining docking and molecular dynamic simulations in drug design. Med. Res. Rev., 2006, 26, 531-568.
-
(2006)
Med. Res. Rev.
, vol.26
, pp. 531-568
-
-
Alonso, H.1
Bliznyuk, A.A.2
Gready, J.E.3
-
152
-
-
6344245774
-
Incorporating protein flexibility instructure-based drug discovery: Using HIV-1 protease as a test case
-
Meagher, K. L.; Carlson, H. A. Incorporating protein flexibility instructure-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
-
153
-
-
18844369136
-
Comparative molecular dynamics simulations of HIV-1 integraseand the T66I/M154I mutant: Binding modes and drug resistance toa diketo acid inhibitor
-
Brigo, A.; Lee, K. W.; Fogolari, F.; Mustata, G. I.; Briggs, J. M.Comparative molecular dynamics simulations of HIV-1 integraseand the T66I/M154I mutant: binding modes and drug resistance toa diketo acid inhibitor. Proteins, 2005, 59, 723-741.
-
(2005)
Proteins
, vol.59
, pp. 723-741
-
-
Brigo, A.1
Lee, K.W.2
Fogolari, F.3
Mustata, G.I.4
Briggs, J.M.5
-
154
-
-
34447258678
-
Structural models of class a G proteincoupledreceptors as a tool for drug design: Insights on transmembranebundle plasticity
-
Deupi, X.; Dolker, N.; Lopez-Rodriguez, M. L.; Campillo, M.; Ballesteros, J. A.; Pardo, L. Structural models of class a G proteincoupledreceptors as a tool for drug design: insights on transmembranebundle plasticity. Curr. Top. Med. Chem., 2007, 7, 991-998.
-
(2007)
Curr. Top. Med. Chem.
, vol.7
, pp. 991-998
-
-
Deupi, X.1
Dolker, N.2
Lopez-Rodriguez, M.L.3
Campillo, M.4
Ballesteros, J.A.5
Pardo, L.6
-
155
-
-
25444444202
-
Computational modeling approachesto structure-function analysis of G protein-coupled receptors
-
Fanelli, F.; De Benedetti, P. G. Computational modeling approachesto structure-function analysis of G protein-coupled receptors.Chem. Rev., 2005, 105, 3297-3351.
-
(2005)
Chem. Rev.
, vol.105
, pp. 3297-3351
-
-
Fanelli, F.1
De Benedetti, P.G.2
-
156
-
-
0030904524
-
Novel methods of sampling phase spacein the simulation of biological systems
-
Berne, B. J.; Straub, J. E. Novel methods of sampling phase spacein the simulation of biological systems. Curr. Opin. Struct. Biol., 1997, 7, 181-189.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 181-189
-
-
Berne, B.J.1
Straub, J.E.2
-
157
-
-
0033117917
-
New Monte Carlo algorithms forprotein folding
-
Hansmann, U. H.; Okamoto, Y. New Monte Carlo algorithms forprotein folding. Curr. Opin. Struct. Biol., 1999, 9, 177-183.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 177-183
-
-
Hansmann, U.H.1
Okamoto, Y.2
-
158
-
-
34147177151
-
Improved sampling methods for molecular simulation
-
Lei, H.; Duan, Y. Improved sampling methods for molecular simulation.Curr. Opin. Struct. Biol., 2007, 17, 187-191.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 187-191
-
-
Lei, H.1
Duan, Y.2
-
159
-
-
0034864528
-
Generalized-ensemblealgorithms for molecular simulations of biopolymers
-
Mitsutake, A.; Sugita, Y.; Okamoto, Y. Generalized-ensemblealgorithms for molecular simulations of biopolymers. Biopolymers, 2001, 60, 96-123.
-
(2001)
Biopolymers
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
160
-
-
1942455272
-
Generalized-ensemble algorithms: Enhanced samplingtechniques for Monte Carlo and molecular dynamics simulations
-
Okamoto, Y. Generalized-ensemble algorithms: enhanced samplingtechniques for Monte Carlo and molecular dynamics simulations. J.Mol. Graph. Model., 2004, 22, 425-439.
-
(2004)
J.Mol. Graph. Model.
, vol.22
, pp. 425-439
-
-
Okamoto, Y.1
-
161
-
-
34547139358
-
Optimized parallel temperingsimulations of proteins
-
Trebst, S.; Troyer, M.; Hansmann, U. H. Optimized parallel temperingsimulations of proteins. J. Chem. Phys., 2006, 124, 174903.
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 174903
-
-
Trebst, S.1
Troyer, M.2
Hansmann, U.H.3
-
162
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini, V. Coarse-grained models for proteins. Curr. Opin. Struct.Biol., 2005, 15, 144-150.
-
(2005)
Curr. Opin. Struct.Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
163
-
-
28844494903
-
Coarse-grained model of proteins incorporating atomistic detail of the active site
-
Neri, M.; Anselmi, C.; Cascella, M.; Maritan, A.; Carloni, P.Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett., 2005, 95, 218102.
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 218102
-
-
Neri, M.1
Anselmi, C.2
Cascella, M.3
Maritan, A.4
Carloni, P.5
-
164
-
-
0025865704
-
Computational studies of ligand diffusionin globins: I
-
Czerminski, R.; Elber, R. Computational studies of ligand diffusionin globins: I. Leghemoglobin. Proteins, 1991, 10, 70-80.
-
(1991)
Leghemoglobin. Proteins
, vol.10
, pp. 70-80
-
-
Czerminski, R.1
Elber, R.2
-
165
-
-
0001616080
-
Replica-exchange molecular dynamicsmethod for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamicsmethod for protein folding. Chem. Phys. Lett., 1999, 314, 141-151.
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
166
-
-
62849084788
-
-
Chipot, C.; Pohorille, A., Eds., Springer, Berlin
-
Chipot, C.; Pohorille, A., Eds. Free Energy Calculations: Theoryand Applications in Chemistry and Biology. Springer, Berlin, 2007.
-
(2007)
Free Energy Calculations: Theoryand Applications in Chemistry and Biology
-
-
-
167
-
-
3142716857
-
Accelerated moleculardynamics: A promising and efficient simulation method forbiomolecules
-
Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated moleculardynamics: a promising and efficient simulation method forbiomolecules. J. Chem. Phys., 2004, 120, 11919-11929.
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
168
-
-
35949020425
-
Replica Monte Carlo simulation of spin glasses
-
Swendsen, R. H.; Wang, J. S. Replica Monte Carlo simulation of spin glasses. Phys. Rev. Lett., 1986, 57, 2607-2609.
-
(1986)
Phys. Rev. Lett.
, vol.57
, pp. 2607-2609
-
-
Swendsen, R.H.1
Wang, J.S.2
-
169
-
-
28844454252
-
Parallel tempering: Theory, applications, and new perspectives
-
Earl, D. J.; Deem, M. W. Parallel tempering: theory, applications, and new perspectives. Phys. Chem. Chem. Phys., 2005, 7, 3910-3916.
-
(2005)
Phys. Chem. Chem. Phys.
, vol.7
, pp. 3910-3916
-
-
Earl, D.J.1
Deem, M.W.2
-
170
-
-
42049109472
-
Computationaltechniques for efficient conformational sampling of proteins
-
Liwo, A.; Czaplewski, C.; Oldziej, S.; Scheraga, H. A. Computationaltechniques for efficient conformational sampling of proteins.Curr. Opin. Struct. Biol., 2008, 18, 134-139.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 134-139
-
-
Liwo, A.1
Czaplewski, C.2
Oldziej, S.3
Scheraga, H.A.4
-
171
-
-
0345133287
-
Folding a protein in a computer: Anatomic description of the folding/unfolding of protein A
-
Garcia, A. E.; Onuchic, J. N. Folding a protein in a computer: anatomic description of the folding/unfolding of protein A. Proc.Natl. Acad. Sci. USA, 2003, 100, 13898-13903.
-
(2003)
Proc.Natl. Acad. Sci. USA
, vol.100
, pp. 13898-13903
-
-
Garcia, A.E.1
Onuchic, J.N.2
-
172
-
-
0036467163
-
Structure of Met-enkephalin inexplicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu, K. Y.; Garcia, A. E. Structure of Met-enkephalin inexplicit aqueous solution using replica exchange molecular dynamics.Proteins, 2002, 46, 225-234.
-
(2002)
Proteins
, vol.46
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
173
-
-
0344824394
-
Trp-cage: Folding free energy landscape in explicit water
-
Zhou, R. Trp-cage: folding free energy landscape in explicit water.Proc. Natl. Acad. Sci. USA, 2003, 100, 13280-13285.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13280-13285
-
-
Zhou, R.1
-
174
-
-
1942455253
-
Exploring the protein folding free energy landscape: Coupling replica exchange method with P3ME/RESPA algorithm
-
Zhou, R. Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm.J. Mol. Graph. Model, 2004, 22, 451-463.
-
(2004)
J. Mol. Graph. Model
, vol.22
, pp. 451-463
-
-
Zhou, R.1
-
175
-
-
0036789950
-
Can a continuum solvent model reproducethe free energy landscape of a beta-hairpin folding in water?
-
Zhou, R.; Berne, B. J. Can a continuum solvent model reproducethe free energy landscape of a beta-hairpin folding in water? Proc.Natl. Acad. Sci. USA, 2002, 99, 12777-12782.
-
(2002)
Proc.Natl. Acad. Sci. USA
, vol.99
, pp. 12777-12782
-
-
Zhou, R.1
Berne, B.J.2
-
176
-
-
0000130835
-
Parallel simulated tempering dynamics of ligand-protein bindingwith ensembles of protein conformations
-
Verkhivker, G.; Rejto, P.; Bouzida, D.; Arthurs, S.; Colson, A.; Freer, S. T.; Gehlhaar, D.; Larson, V.; Luty, B.; Marrone, T.; Rose, P. Parallel simulated tempering dynamics of ligand-protein bindingwith ensembles of protein conformations. Chem. Phys. Lett., 2001, 337, 181-189.
-
(2001)
Chem. Phys. Lett.
, vol.337
, pp. 181-189
-
-
Verkhivker, G.1
Rejto, P.2
Bouzida, D.3
Arthurs, S.4
Colson, A.5
Freer, S.T.6
Gehlhaar, D.7
Larson, V.8
Luty, B.9
Marrone, T.10
Rose, P.11
-
177
-
-
34548259669
-
Drug discovery using gridtechnology
-
In, Starikov, E., Lewis, J. and Tanaka, S.; Eds.; Elsevier: Amsterdam
-
Goto, H.; Obata, S.; Kamakura, T.; Nakayama, N.; Sato, M.; Nakajima, Y.; Nagashima, U.; Watanabe, T.; Inadomi, Y.; Ito, M.; Nishikawa, T.; Nakano, T.; Nilsson, L.; Tanaka, S.; Fukuzawa, K.; Inagaki, Y.; Hamada, M.; Chuman, H. Drug discovery using gridtechnology. In Modern Methods for Theoretical Physical Chemistryof Biopolymers; Starikov, E., Lewis, J. and Tanaka, S.; Eds.; Elsevier: Amsterdam, 2006, pp 227-248.
-
(2006)
Modern Methods for Theoretical Physical Chemistryof Biopolymers
, pp. 227-248
-
-
Goto, H.1
Obata, S.2
Kamakura, T.3
Nakayama, N.4
Sato, M.5
Nakajima, Y.6
Nagashima, U.7
Watanabe, T.8
Inadomi, Y.9
Ito, M.10
Nishikawa, T.11
Nakano, T.12
Nilsson, L.13
Tanaka, S.14
Fukuzawa, K.15
Inagaki, Y.16
Hamada, M.17
Chuman, H.18
-
178
-
-
25444481354
-
Replica exchangewith solute tempering: A method for sampling biological systems inexplicit water
-
Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Replica exchangewith solute tempering: a method for sampling biological systems inexplicit water. Proc. Natl. Acad. Sci. USA, 2005, 102, 13749-13754.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13749-13754
-
-
Liu, P.1
Kim, B.2
Friesner, R.A.3
Berne, B.J.4
-
179
-
-
18544381108
-
Modified replicaexchange simulation methods for local structure refinement
-
Cheng, X.; Cui, G.; Hornak, V.; Simmerling, C. Modified replicaexchange simulation methods for local structure refinement. J.Phys. Chem. B, 2005, 109, 8220-8230.
-
(2005)
J.Phys. Chem. B
, vol.109
, pp. 8220-8230
-
-
Cheng, X.1
Cui, G.2
Hornak, V.3
Simmerling, C.4
-
180
-
-
27144440086
-
Efficient sampling of protein structuresby model hopping
-
Kwak, W.; Hansmann, U. H. Efficient sampling of protein structuresby model hopping. Phys. Rev. Lett., 2005, 95, 138102.
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 138102
-
-
Kwak, W.1
Hansmann, U.H.2
-
181
-
-
42149182885
-
Hamiltonian replica exchange moleculardynamics using soft-core interactions
-
Hritz, J.; Oostenbrink, C. Hamiltonian replica exchange moleculardynamics using soft-core interactions. J. Chem. Phys., 2008, 128, 144121.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 144121
-
-
Hritz, J.1
Oostenbrink, C.2
-
182
-
-
54849417403
-
Calculation of absoluteprotein-ligand binding free energy using distributed replica sampling
-
Rodinger, T.; Howell, P. L.; Pomes, R. Calculation of absoluteprotein-ligand binding free energy using distributed replica sampling.J. Chem. Phys., 2008, 129, 155102.
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 155102
-
-
Rodinger, T.1
Howell, P.L.2
Pomes, R.3
-
183
-
-
0346350789
-
The development of replicaexchange-based free-energy methods
-
Woods, C.; Essex, J.; King, M. The development of replicaexchange-based free-energy methods. J. Phys. Chem, B, 2003, 107, 13703-13710.
-
(2003)
J. Phys. Chem, B
, vol.107
, pp. 13703-13710
-
-
Woods, C.1
Essex, J.2
King, M.3
-
184
-
-
58149158233
-
Accelerating conformationaltransitions in biomolecular systems
-
Hamelberg, D.; McCammon, J. A. Accelerating conformationaltransitions in biomolecular systems. Ann. Rep. Comp. Chem., 2006, 2, 221-232.
-
(2006)
Ann. Rep. Comp. Chem.
, vol.2
, pp. 221-232
-
-
Hamelberg, D.1
McCammon, J.A.2
-
185
-
-
1442281293
-
A method for accelerating the molecular dynamics simulationof infrequent events
-
Voter, A. A method for accelerating the molecular dynamics simulationof infrequent events. J. Chem. Phys., 1997, 106, 4665-4677.
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 4665-4677
-
-
Voter, A.1
-
186
-
-
34247500337
-
Exploring multipletimescale motions in protein GB3 using accelerated moleculardynamics and NMR spectroscopy
-
Markwick, P. R.; Bouvignies, G.; Blackledge, M. Exploring multipletimescale motions in protein GB3 using accelerated moleculardynamics and NMR spectroscopy. J. Am. Chem. Soc., 2007, 129, 4724-4730.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 4724-4730
-
-
Markwick, P.R.1
Bouvignies, G.2
Blackledge, M.3
-
187
-
-
63549096871
-
Ras conformationalswitching: Simulating nucleotide-dependent conformational transitionswith accelerated molecular dynamics
-
Grant, B. J.; Gorfe, A. A.; McCammon, J. A. Ras conformationalswitching: simulating nucleotide-dependent conformational transitionswith accelerated molecular dynamics. PLoS Comput. Biol., 2009, 5, e1000325.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Grant, B.J.1
Gorfe, A.A.2
McCammon, J.A.3
-
188
-
-
61949111766
-
Thermodynamics and foldingpathways of trpzip2: An accelerated molecular dynamics simulationstudy
-
Yang, L.; Shao, Q.; Gao, Y. Q. Thermodynamics and foldingpathways of trpzip2: an accelerated molecular dynamics simulationstudy. J. Phys. Chem. B, 2009, 113, 803-808.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 803-808
-
-
Yang, L.1
Shao, Q.2
Gao, Y.Q.3
-
190
-
-
34848879539
-
The conformational free energy landscape of beta-Dglucopyranose.Implications for substrate preactivation in betaglucosidehydrolases
-
Biarnes, X.; Ardevol, A.; Planas, A.; Rovira, C.; Laio, A.; Parrinello, M. The conformational free energy landscape of beta-Dglucopyranose.Implications for substrate preactivation in betaglucosidehydrolases. J. Am. Chem. Soc., 2007, 129, 10686-10693.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 10686-10693
-
-
Biarnes, X.1
Ardevol, A.2
Planas, A.3
Rovira, C.4
Laio, A.5
Parrinello, M.6
-
191
-
-
47749110306
-
Conformational changes and gating at the selectivity filterof potassium channels
-
Domene, C.; Klein, M. L.; Branduardi, D.; Gervasio, F. L.; Parrinello, M. Conformational changes and gating at the selectivity filterof potassium channels. J. Am. Chem. Soc., 2008, 130, 9474-9480.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 9474-9480
-
-
Domene, C.1
Klein, M.L.2
Branduardi, D.3
Gervasio, F.L.4
Parrinello, M.5
-
192
-
-
33749519366
-
Using metadynamicsto understand the mechanism of calmodulin/target recognitionat atomic detail
-
Fiorin, G.; Pastore, A.; Carloni, P.; Parrinello, M. Using metadynamicsto understand the mechanism of calmodulin/target recognitionat atomic detail. Biophys. J., 2006, 91, 2768-2777.
-
(2006)
Biophys. J.
, vol.91
, pp. 2768-2777
-
-
Fiorin, G.1
Pastore, A.2
Carloni, P.3
Parrinello, M.4
-
193
-
-
38549176824
-
The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterasegorge
-
Petraglio, G.; Bartolini, M.; Branduardi, D.; Andrisano, V.; Recanatini, M.; Gervasio, F. L.; Cavalli, A.; Parrinello, M. The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterasegorge. Proteins, 2008, 70, 779-785.
-
(2008)
Proteins
, vol.70
, pp. 779-785
-
-
Petraglio, G.1
Bartolini, M.2
Branduardi, D.3
Andrisano, V.4
Recanatini, M.5
Gervasio, F.L.6
Cavalli, A.7
Parrinello, M.8
-
194
-
-
33751248251
-
Stability and structure of oligomers of the Alzheimer peptide Abeta 16-22: From the dimer to the 32-mer
-
Rohrig, U. F.; Laio, A.; Tantalo, N.; Parrinello, M.; Petronzio, R.Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer. Biophys. J., 2006, 91, 3217-3229.
-
(2006)
Biophys. J.
, vol.91
, pp. 3217-3229
-
-
Rohrig, U.F.1
Laio, A.2
Tantalo, N.3
Parrinello, M.4
Petronzio, R.5
-
195
-
-
43249123138
-
Metadynamicssimulations of the high-pressure phases of silicon employing ahigh-dimensional neural network potential
-
Behler, J.; Martonak, R.; Donadio, D.; Parrinello, M. Metadynamicssimulations of the high-pressure phases of silicon employing ahigh-dimensional neural network potential. Phys. Rev. Lett., 2008, 100, 185501.
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 185501
-
-
Behler, J.1
Martonak, R.2
Donadio, D.3
Parrinello, M.4
-
196
-
-
33746326814
-
Solid-statephase transition induced by pressure in LiOH x H2O
-
Di Pietro, E.; Pagliai, M.; Cardini, G.; Schettino, V. Solid-statephase transition induced by pressure in LiOH x H2O. J. Phys.Chem. B, 2006, 110, 13539-13546.
-
(2006)
J. Phys.Chem. B
, vol.110
, pp. 13539-13546
-
-
Di Pietro, E.1
Pagliai, M.2
Cardini, G.3
Schettino, V.4
-
197
-
-
42749102127
-
Ab initio simulations of photoinduced interconversions of oxygen deficient centers inamorphous silica
-
Donadio, D.; Bernasconi, M.; Boero, M. Ab initio simulations of photoinduced interconversions of oxygen deficient centers inamorphous silica. Phys. Rev. Lett., 2001, 87, 195504.
-
(2001)
Phys. Rev. Lett.
, vol.87
, pp. 195504
-
-
Donadio, D.1
Bernasconi, M.2
Boero, M.3
-
198
-
-
41049098084
-
Liquid-solid coexistence via themetadynamics approach
-
Prestipino, S.; Giaquinta, P. V. Liquid-solid coexistence via themetadynamics approach. J. Chem. Phys., 2008, 128, 114-707.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 114-707
-
-
Prestipino, S.1
Giaquinta, P.V.2
-
199
-
-
3142678009
-
Constant pressure reactivemolecular dynamics simulations of phase transitions under pressure: The graphite to diamond conversion revisited
-
Zipoli, F.; Bernasconi, M.; Martonak, R. Constant pressure reactivemolecular dynamics simulations of phase transitions under pressure: The graphite to diamond conversion revisited. Eur. Phys. J. B, 2004, 39, 41-47.
-
(2004)
Eur. Phys. J. B
, vol.39
, pp. 41-47
-
-
Zipoli, F.1
Bernasconi, M.2
Martonak, R.3
-
200
-
-
46149096158
-
The thermal stability of lattice-energy minima of 5-fluorouracil: Metadynamics as an aid to polymorph prediction
-
Karamertzanis, P. G.; Raiteri, P.; Parrinello, M.; Leslie, M.; Price, S. L. The thermal stability of lattice-energy minima of 5-fluorouracil: metadynamics as an aid to polymorph prediction. J.Phys. Chem. B, 2008, 112, 4298-4308.
-
(2008)
J.Phys. Chem. B
, vol.112
, pp. 4298-4308
-
-
Karamertzanis, P.G.1
Raiteri, P.2
Parrinello, M.3
Leslie, M.4
Price, S.L.5
-
201
-
-
33746609016
-
Crystalstructure transformations in SiO2 from classical and ab initiometadynamics
-
Martonak, R.; Donadio, D.; Oganov, A. R.; Parrinello, M. Crystalstructure transformations in SiO2 from classical and ab initiometadynamics. Nat. Mater., 2006, 5, 623-626.
-
(2006)
Nat. Mater.
, vol.5
, pp. 623-626
-
-
Martonak, R.1
Donadio, D.2
Oganov, A.R.3
Parrinello, M.4
-
202
-
-
20144372370
-
Simulation of structural phase transitionsby metadynamics
-
Martonak, R.; Laio, A.; Bernasconi, M.; Ceriani, C.; Raiteri, P.; ZIpoli, F.; Parrinello, M. Simulation of structural phase transitionsby metadynamics. Zeitschrift für Kristallographie 2005, 220, 489-498.
-
(2005)
Zeitschrift für Kristallographie
, vol.220
, pp. 489-498
-
-
Martonak, R.1
Laio, A.2
Bernasconi, M.3
Ceriani, C.4
Raiteri, P.5
ZIpoli, F.6
Parrinello, M.7
-
203
-
-
29244487921
-
Anisotropy of Earth's D" layer and stacking faults in the MgSiO3post-perovskite phase
-
Oganov, A. R.; Martonak, R.; Laio, A.; Raiteri, P.; Parrinello, M.Anisotropy of Earth's D" layer and stacking faults in the MgSiO3post-perovskite phase. Nature, 2005, 438, 1142-1144.
-
(2005)
Nature
, vol.438
, pp. 1142-1144
-
-
Oganov, A.R.1
Martonak, R.2
Laio, A.3
Raiteri, P.4
Parrinello, M.5
-
204
-
-
33746191904
-
Formamide hydrolysis inalkaline aqueous solution: Insight from Ab initio metadynamicscalculations
-
Blumberger, J.; Ensing, B.; Klein, M. L. Formamide hydrolysis inalkaline aqueous solution: insight from Ab initio metadynamicscalculations. Angew. Chem. Int. Ed. Engl., 2006, 45, 2893-2897.
-
(2006)
Angew. Chem. Int. Ed. Engl.
, vol.45
, pp. 2893-2897
-
-
Blumberger, J.1
Ensing, B.2
Klein, M.L.3
-
205
-
-
33644968698
-
Metadynamicsas a tool for exploring free energy landscapes of chemicalreactions
-
Ensing, B.; De Vivo, M.; Liu, Z.; Moore, P.; Klein, M. L. Metadynamicsas a tool for exploring free energy landscapes of chemicalreactions. Acc. Chem. Res., 2006, 39, 73-81.
-
(2006)
Acc. Chem. Res.
, vol.39
, pp. 73-81
-
-
Ensing, B.1
De Vivo, M.2
Liu, Z.3
Moore, P.4
Klein, M.L.5
-
206
-
-
3543055345
-
Aminimum free energy reaction path for the E2 reaction betweenfluoro ethane and a fluoride ion
-
Ensing, B.; Laio, A.; Gervasio, F. L.; Parrinello, M.; Klein, M. L. Aminimum free energy reaction path for the E2 reaction betweenfluoro ethane and a fluoride ion. J. Am. Chem. Soc., 2004, 126, 9492-9493.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 9492-9493
-
-
Ensing, B.1
Laio, A.2
Gervasio, F.L.3
Parrinello, M.4
Klein, M.L.5
-
207
-
-
33947184342
-
Free energy ab initio metadynamics: A new tool for thetheoretical study of organometallic reactivity? Example of the C-Cand C-H reductive eliminations from platinum(IV) complexes
-
Michel, C.; Laio, A.; Mohamed, F.; Krack, M.; Parrinello, M.; Milet, A. Free energy ab initio metadynamics: A new tool for thetheoretical study of organometallic reactivity? Example of the C-Cand C-H reductive eliminations from platinum(IV) complexes. Organometallics, 2007, 26, 1241-1249.
-
(2007)
Organometallics
, vol.26
, pp. 1241-1249
-
-
Michel, C.1
Laio, A.2
Mohamed, F.3
Krack, M.4
Parrinello, M.5
Milet, A.6
-
208
-
-
40949136532
-
Influence of extreme thermodynamicconditions and pyrite surfaces on peptide synthesis inaqueous media
-
Schreiner, E.; Nair, N. N.; Marx, D. Influence of extreme thermodynamicconditions and pyrite surfaces on peptide synthesis inaqueous media. J. Am. Chem. Soc., 2008, 130, 2768-2770.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 2768-2770
-
-
Schreiner, E.1
Nair, N.N.2
Marx, D.3
-
209
-
-
33748517436
-
Freezing of a Lennard-Jonesfluid: From nucleation to spinodal regime
-
Trudu, F.; Donadio, D.; Parrinello, M. Freezing of a Lennard-Jonesfluid: from nucleation to spinodal regime. Phys. Rev. Lett., 2006, 97, 105701.
-
(2006)
Phys. Rev. Lett.
, vol.97
, pp. 105701
-
-
Trudu, F.1
Donadio, D.2
Parrinello, M.3
-
210
-
-
34147097967
-
Metadynamics in essentialcoordinates: Free energy simulation of conformational changes
-
Spiwok, V.; Lipovova, P.; Kralova, B. Metadynamics in essentialcoordinates: free energy simulation of conformational changes. J.Phys. Chem. B, 2007, 111, 3073-3076.
-
(2007)
J.Phys. Chem. B
, vol.111
, pp. 3073-3076
-
-
Spiwok, V.1
Lipovova, P.2
Kralova, B.3
-
211
-
-
34249071886
-
A bias-exchange approach to protein folding
-
Piana, S.; Laio, A. A bias-exchange approach to protein folding. J.Phys. Chem. B, 2007, 111, 4553-4559.
-
(2007)
J.Phys. Chem. B
, vol.111
, pp. 4553-4559
-
-
Piana, S.1
Laio, A.2
-
212
-
-
33750040264
-
Free-energylandscape for beta hairpin folding from combined parallel temperingand metadynamics
-
Bussi, G.; Gervasio, F. L.; Laio, A.; Parrinello, M. Free-energylandscape for beta hairpin folding from combined parallel temperingand metadynamics. J. Am. Chem. Soc., 2006, 128, 13435-13441.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 13435-13441
-
-
Bussi, G.1
Gervasio, F.L.2
Laio, A.3
Parrinello, M.4
-
213
-
-
14744276066
-
Flexible docking in solutionusing metadynamics
-
Gervasio, F. L.; Laio, A.; Parrinello, M. Flexible docking in solutionusing metadynamics. J. Am. Chem. Soc., 2005, 127, 2600-2607.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 2600-2607
-
-
Gervasio, F.L.1
Laio, A.2
Parrinello, M.3
-
214
-
-
35348964604
-
Insight into the folding inhibition of the HIV-1 proteaseby a small peptide
-
Bonomi, M.; Gervasio, F. L.; Tiana, G.; Provasi, D.; Broglia, R. A.; Parrinello, M. Insight into the folding inhibition of the HIV-1 proteaseby a small peptide. Biophys. J., 2007, 93, 2813-2821.
-
(2007)
Biophys. J.
, vol.93
, pp. 2813-2821
-
-
Bonomi, M.1
Gervasio, F.L.2
Tiana, G.3
Provasi, D.4
Broglia, R.A.5
Parrinello, M.6
-
215
-
-
3042772813
-
Microscopicmechanism of antibiotics translocation through a porin
-
Ceccarelli, M.; Danelon, C.; Laio, A.; Parrinello, M. Microscopicmechanism of antibiotics translocation through a porin. Biophys. J., 2004, 87, 58-64.
-
(2004)
Biophys. J.
, vol.87
, pp. 58-64
-
-
Ceccarelli, M.1
Danelon, C.2
Laio, A.3
Parrinello, M.4
-
216
-
-
21244439384
-
The role of the peripheral anionic site and cation-pi interactionsin the ligand penetration of the human AChE gorge
-
Branduardi, D.; Gervasio, F. L.; Cavalli, A.; Recanatini, M.; Parrinello, M. The role of the peripheral anionic site and cation-pi interactionsin the ligand penetration of the human AChE gorge. J.Am. Chem. Soc., 2005, 127, 9147-9155.
-
(2005)
J.Am. Chem. Soc.
, vol.127
, pp. 9147-9155
-
-
Branduardi, D.1
Gervasio, F.L.2
Cavalli, A.3
Recanatini, M.4
Parrinello, M.5
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