-
1
-
-
64849111005
-
Sending Signals Dynamically
-
Smock, R. G.; Gierasch, L. M. Sending Signals Dynamically Science 2009, 324, 198-203
-
(2009)
Science
, vol.324
, pp. 198-203
-
-
Smock, R.G.1
Gierasch, L.M.2
-
2
-
-
77951270272
-
Large conformational changes in proteins: Signaling and other functions
-
Grant, B. J.; Gorfe, A. A.; McCammon, J. A. Large conformational changes in proteins: signaling and other functions Curr. Opin. Struct. Biol. 2010, 20, 142-147
-
(2010)
Curr. Opin. Struct. Biol.
, vol.20
, pp. 142-147
-
-
Grant, B.J.1
Gorfe, A.A.2
McCammon, J.A.3
-
3
-
-
77957937199
-
Atomic-Level Characterization of the Structural Dynamics of Proteins
-
Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan, Y.; Wriggers, W. Atomic-Level Characterization of the Structural Dynamics of Proteins Science 2010, 330, 341-346
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.O.5
Eastwood, M.P.6
Bank, J.A.7
Jumper, J.M.8
Salmon, J.K.9
Shan, Y.10
Wriggers, W.11
-
4
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method 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
-
5
-
-
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
-
8
-
-
78049264030
-
A self-learning algorithm for biased molecular dynamics
-
Tribello, G. A.; Ceriotti, M.; Parrinello, M. A self-learning algorithm for biased molecular dynamics Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 17509-17514
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 17509-17514
-
-
Tribello, G.A.1
Ceriotti, M.2
Parrinello, M.3
-
9
-
-
3142716857
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules 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
-
10
-
-
84866146945
-
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
-
Pierce, L. C. T.; Salomon-Ferrer, R.; de Oliveira, C. A. F.; McCammon, J. A.; Walker, R. C. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics J. Chem. Theory Comput. 2012, 8, 2997-3002
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2997-3002
-
-
Pierce, L.C.T.1
Salomon-Ferrer, R.2
De Oliveira, C.A.F.3
McCammon, J.A.4
Walker, R.C.5
-
11
-
-
77950448255
-
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics
-
Abrams, C. F.; Vanden-Eijnden, E. Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 4961-4966
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 4961-4966
-
-
Abrams, C.F.1
Vanden-Eijnden, E.2
-
12
-
-
77950102787
-
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
-
Henin, J.; Fiorin, G.; Chipot, C.; Klein, M. L. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables J. Chem. Theory Comput. 2010, 6, 35-47
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 35-47
-
-
Henin, J.1
Fiorin, G.2
Chipot, C.3
Klein, M.L.4
-
13
-
-
33750970357
-
A second look at canonical sampling of biomolecules using replica exchange simulation
-
Zuckerman, D. M.; Lyman, E. A second look at canonical sampling of biomolecules using replica exchange simulation J. Chem. Theory Comput. 2006, 2, 1200-1202
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1200-1202
-
-
Zuckerman, D.M.1
Lyman, E.2
-
14
-
-
34848892169
-
Simulating replica exchange simulations of protein folding with a kinetic network model
-
Zheng, W. H.; Andrec, M.; Gallicchio, E.; Levy, R. M. Simulating replica exchange simulations of protein folding with a kinetic network model Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 15340-15345
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 15340-15345
-
-
Zheng, W.H.1
Andrec, M.2
Gallicchio, E.3
Levy, R.M.4
-
15
-
-
44449093098
-
Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment
-
Huang, X. H.; Bowman, G. R.; Pande, V. S. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment J. Chem. Phys. 2008, 128 205106
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 205106
-
-
Huang, X.H.1
Bowman, G.R.2
Pande, V.S.3
-
16
-
-
46549088884
-
How efficient is replica exchange molecular dynamics? An analytic approach
-
Nymeyer, H. How efficient is replica exchange molecular dynamics? An analytic approach J. Chem. Theory Comput. 2008, 4, 626-636
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 626-636
-
-
Nymeyer, H.1
-
17
-
-
72049094568
-
Error and efficiency of replica exchange molecular dynamics simulations
-
Rosta, E.; Hummer, G. Error and efficiency of replica exchange molecular dynamics simulations J. Chem. Phys. 2009, 131 165102
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 165102
-
-
Rosta, E.1
Hummer, G.2
-
18
-
-
84859478167
-
Using sketch-map coordinates to analyze and bias molecular dynamics simulations
-
Tribello, G. A.; Ceriotti, M.; Parrinello, M. Using sketch-map coordinates to analyze and bias molecular dynamics simulations Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 5196-5201
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 5196-5201
-
-
Tribello, G.A.1
Ceriotti, M.2
Parrinello, M.3
-
19
-
-
3042545299
-
Computing time scales from reaction coordinates by milestoning
-
Faradjian, A. K.; Elber, R. Computing time scales from reaction coordinates by milestoning J. Chem. Phys. 2004, 120, 10880-10889
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 10880-10889
-
-
Faradjian, A.K.1
Elber, R.2
-
20
-
-
79952096187
-
Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI
-
Ovchinnikov, V.; Karplus, M.; Vanden-Eijnden, E. Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI J. Chem. Phys. 2011, 134 085103
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 085103
-
-
Ovchinnikov, V.1
Karplus, M.2
Vanden-Eijnden, E.3
-
22
-
-
0000729781
-
Transition path sampling and the calculation of rate constants
-
Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. Transition path sampling and the calculation of rate constants J. Chem. Phys. 1998, 108, 1964-1977
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 1964-1977
-
-
Dellago, C.1
Bolhuis, P.G.2
Csajka, F.S.3
Chandler, D.4
-
23
-
-
84859551481
-
Transition path sampling of protein conformational changes
-
Juraszek, J.; Vreede, J.; Bolhuis, P. G. Transition path sampling of protein conformational changes Chem. Phys. 2012, 396, 30-44
-
(2012)
Chem. Phys.
, vol.396
, pp. 30-44
-
-
Juraszek, J.1
Vreede, J.2
Bolhuis, P.G.3
-
24
-
-
36749060078
-
Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
-
Zhang, B. W.; Jasnow, D.; Zuckerman, D. M. Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 18043-18048
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 18043-18048
-
-
Zhang, B.W.1
Jasnow, D.2
Zuckerman, D.M.3
-
25
-
-
78149441109
-
Heterogeneous Path Ensembles for Conformational Transitions in Semiatomistic Models of Adenylate Kinase
-
Bhatt, D.; Zuckerman, D. M. Heterogeneous Path Ensembles for Conformational Transitions in Semiatomistic Models of Adenylate Kinase J. Chem. Theory Comput. 2010, 6, 3527-3539
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3527-3539
-
-
Bhatt, D.1
Zuckerman, D.M.2
-
26
-
-
77952343449
-
Dual Grid Methods for Finding the Reaction Path on Reduced Potential Energy Surfaces
-
Burger, S. K.; Ayers, P. W. Dual Grid Methods for Finding the Reaction Path on Reduced Potential Energy Surfaces J. Chem. Theory Comput. 2010, 6, 1490-1497
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1490-1497
-
-
Burger, S.K.1
Ayers, P.W.2
-
27
-
-
36749008588
-
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
-
Arora, K.; Brooks, C. L. Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 18496-18501
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 18496-18501
-
-
Arora, K.1
Brooks, C.L.2
-
28
-
-
37649023990
-
Improving the efficiency of the NEB reaction path finding algorithm
-
Galvan, I. F.; Field, M. J. Improving the efficiency of the NEB reaction path finding algorithm J. Comput. Chem. 2008, 29, 139-143
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 139-143
-
-
Galvan, I.F.1
Field, M.J.2
-
29
-
-
0027794972
-
Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ↔ R Transition in Insulin
-
Schlitter, J.; Engels, M.; Kruger, P.; Jacoby, E.; Wollmer, A. Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ↔ R Transition in Insulin Mol. Simul. 1993, 10, 291-308
-
(1993)
Mol. Simul.
, vol.10
, pp. 291-308
-
-
Schlitter, J.1
Engels, M.2
Kruger, P.3
Jacoby, E.4
Wollmer, A.5
-
30
-
-
0030059225
-
Ligand binding: Molecular mechanics calculation of the streptavidin biotin rupture force
-
Grubmuller, H.; Heymann, B.; Tavan, P. Ligand binding: Molecular mechanics calculation of the streptavidin biotin rupture force Science 1996, 271, 997-999
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmuller, H.1
Heymann, B.2
Tavan, P.3
-
31
-
-
0035312645
-
Steered molecular dynamics and mechanical functions of proteins
-
Isralewitz, B.; Gao, M.; Schulten, K. Steered molecular dynamics and mechanical functions of proteins Curr. Opin. Struct. Biol. 2001, 11, 224-230
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 224-230
-
-
Isralewitz, B.1
Gao, M.2
Schulten, K.3
-
32
-
-
73949085678
-
Rapid equilibrium sampling initiated from nonequilibrium data
-
Huang, X.; Bowman, G. R.; Bacallado, S.; Pande, V. S. Rapid equilibrium sampling initiated from nonequilibrium data Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 19765-19769
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 19765-19769
-
-
Huang, X.1
Bowman, G.R.2
Bacallado, S.3
Pande, V.S.4
-
33
-
-
62649161772
-
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
-
Yang, S.; Banavali, N. K.; Roux, B. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 3776-3781
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 3776-3781
-
-
Yang, S.1
Banavali, N.K.2
Roux, B.3
-
34
-
-
63749086305
-
ErbB receptors and signaling pathways in cancer
-
Hynes, N. E.; MacDonald, G. ErbB receptors and signaling pathways in cancer Curr. Opin. Cell Biol. 2009, 21, 177-184
-
(2009)
Curr. Opin. Cell Biol.
, vol.21
, pp. 177-184
-
-
Hynes, N.E.1
Macdonald, G.2
-
35
-
-
79953308071
-
Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms
-
Jura, N.; Zhang, X. W.; Endres, N. F.; Seeliger, M. A.; Schindler, T.; Kuriyan, J. Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms Mol. Cell 2011, 42, 9-22
-
(2011)
Mol. Cell
, vol.42
, pp. 9-22
-
-
Jura, N.1
Zhang, X.W.2
Endres, N.F.3
Seeliger, M.A.4
Schindler, T.5
Kuriyan, J.6
-
36
-
-
62549151081
-
Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations
-
Berteotti, A.; Cavalli, A.; Branduardi, D.; Gervasio, F. L.; Recanatini, M.; Parrinello, M. Protein Conformational Transitions: The Closure 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
-
37
-
-
58549114067
-
A conserved protonation-dependent switch controls drug binding in the Abl kinase
-
Shan, Y. B.; Seeliger, M. A.; Eastwood, M. P.; Frank, F.; Xu, H. F.; Jensen, M. O.; Dror, R. O.; Kuriyan, J.; Shaw, D. E. A conserved protonation-dependent switch controls drug binding in the Abl kinase Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 139-144
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 139-144
-
-
Shan, Y.B.1
Seeliger, M.A.2
Eastwood, M.P.3
Frank, F.4
Xu, H.F.5
Jensen, M.O.6
Dror, R.O.7
Kuriyan, J.8
Shaw, D.E.9
-
38
-
-
84859961776
-
αc Helix as a Switch in the Conformational Transition of Src/CDK-like Kinase Domains
-
Huang, H.; Zhao, R. J.; Dickson, B. M.; Skeel, R. D.; Post, C. B. αC Helix as a Switch in the Conformational Transition of Src/CDK-like Kinase Domains J. Phys. Chem. B 2012, 116, 4465-4475
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 4465-4475
-
-
Huang, H.1
Zhao, R.J.2
Dickson, B.M.3
Skeel, R.D.4
Post, C.B.5
-
39
-
-
84864247160
-
Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions
-
Johnson, M. E.; Hummer, G. Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions J. Phys. Chem. B 2012, 116, 8573-8583
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 8573-8583
-
-
Johnson, M.E.1
Hummer, G.2
-
40
-
-
84856694630
-
The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation
-
Lovera, S.; Sutto, L.; Boubeva, R.; Scapozza, L.; Dolker, N.; Gervasio, F. L. The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation J. Am. Chem. Soc. 2012, 134, 2496-2499
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 2496-2499
-
-
Lovera, S.1
Sutto, L.2
Boubeva, R.3
Scapozza, L.4
Dolker, N.5
Gervasio, F.L.6
-
41
-
-
84859922106
-
″dFG-Flip″ in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop
-
Vashisth, H.; Maragliano, L.; Abrams, C. F. ″DFG-Flip″ in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop Biophys. J. 2012, 102, 1979-1987
-
(2012)
Biophys. J.
, vol.102
, pp. 1979-1987
-
-
Vashisth, H.1
Maragliano, L.2
Abrams, C.F.3
-
42
-
-
84876902448
-
Transitions to catalytically inactive conformations in EGFR kinase
-
Shan, Y. B.; Arkhipov, A.; Kim, E. T.; Pan, A. C.; Shaw, D. E. Transitions to catalytically inactive conformations in EGFR kinase Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 7270-7275
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 7270-7275
-
-
Shan, Y.B.1
Arkhipov, A.2
Kim, E.T.3
Pan, A.C.4
Shaw, D.E.5
-
43
-
-
84879510153
-
Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase
-
Sutto, L.; Luigi Gervasio, F. Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 10616-10621
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 10616-10621
-
-
Sutto, L.1
Luigi Gervasio, F.2
-
44
-
-
33646755174
-
A Src-like inactive conformation 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 inactive conformation in the Abl tyrosine kinase domain PLoS Biol. 2006, 4, 753-767
-
(2006)
PLoS Biol.
, vol.4
, pp. 753-767
-
-
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
-
45
-
-
33847406095
-
Structures of lung cancer-derived EGFR mutants and inhibitor complexes: Mechanism of activation and insights into differential inhibitor sensitivity
-
Yun, C. H.; Boggon, T. J.; Li, Y. Q.; Woo, M. S.; Greulich, H.; Meyerson, M.; Eck, M. J. Structures of lung cancer-derived EGFR mutants and inhibitor complexes: Mechanism of activation and insights into differential inhibitor sensitivity Cancer Cell 2007, 11, 217-227
-
(2007)
Cancer Cell
, vol.11
, pp. 217-227
-
-
Yun, C.H.1
Boggon, T.J.2
Li, Y.Q.3
Woo, M.S.4
Greulich, H.5
Meyerson, M.6
Eck, M.J.7
-
46
-
-
84875754212
-
Design and synthesis of novel pyrimido 4,5-b azepine derivatives as HER2/EGFR dual inhibitors
-
Kawakita, Y.; Seto, M.; Ohashi, T.; Tamura, T.; Yusa, T.; Miki, H.; Iwata, H.; Kamiguchi, H.; Tanaka, T.; Sogabe, S.; Ohta, Y.; Ishikawa, T. Design and synthesis of novel pyrimido 4,5-b azepine derivatives as HER2/EGFR dual inhibitors Biorg. Med. Chem. 2013, 21, 2250-2261
-
(2013)
Biorg. Med. Chem.
, vol.21
, pp. 2250-2261
-
-
Kawakita, Y.1
Seto, M.2
Ohashi, T.3
Tamura, T.4
Yusa, T.5
Miki, H.6
Iwata, H.7
Kamiguchi, H.8
Tanaka, T.9
Sogabe, S.10
Ohta, Y.11
Ishikawa, T.12
-
47
-
-
84873406911
-
Insights into the Aberrant Activity of Mutant EGFR Kinase Domain and Drug Recognition
-
Gajiwala, K. S.; Feng, J. L.; Ferre, R.; Ryan, K.; Brodsky, O.; Weinrich, S.; Kath, J. C.; Stewart, A. Insights into the Aberrant Activity of Mutant EGFR Kinase Domain and Drug Recognition Structure 2013, 21, 209-219
-
(2013)
Structure
, vol.21
, pp. 209-219
-
-
Gajiwala, K.S.1
Feng, J.L.2
Ferre, R.3
Ryan, K.4
Brodsky, O.5
Weinrich, S.6
Kath, J.C.7
Stewart, A.8
-
48
-
-
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
-
49
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. 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
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.M.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.M.12
Kollman, P.13
-
50
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model Proteins: Struct., Funct., Bioinf. 2004, 55, 383-394
-
(2004)
Proteins: Struct., Funct., Bioinf.
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
51
-
-
33646940952
-
Numerical-integration of 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 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
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method J. Chem. Phys. 1995, 103, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
53
-
-
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
-
54
-
-
84860767348
-
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
-
Gotz, A. W.; Williamson, M. J.; Xu, D.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born J. Chem. Theory Comput. 2012, 8, 1542-1555
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1542-1555
-
-
Gotz, A.W.1
Williamson, M.J.2
Xu, D.3
Poole, D.4
Le Grand, S.5
Walker, R.C.6
-
55
-
-
84884192184
-
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
-
Salomon-Ferrer, R.; Götz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald J. Chem. Theory Comput. 2013, 9, 3878-3888
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3878-3888
-
-
Salomon-Ferrer, R.1
Götz, A.W.2
Poole, D.3
Le Grand, S.4
Walker, R.C.5
-
56
-
-
84880022273
-
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
-
Roe, D. R.; Cheatham, T. E. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013, 9, 3084-3095
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3084-3095
-
-
Roe, D.R.1
Cheatham, T.E.2
-
57
-
-
0002607026
-
Bayesian classification (AutoClass): Theory and results
-
Fayyad, U. M. Piatetsky-Shapiro, G. Smyth, P. Uthurusamy, R. MIT Press: Cambridge, MA, USA
-
Cheeseman, P.; Stutz, J. Bayesian classification (AutoClass): Theory and results. In Advances in knowledge discovery and data mining; Fayyad, U. M.; Piatetsky-Shapiro, G.; Smyth, P.; Uthurusamy, R., Eds.; MIT Press: Cambridge, MA, USA, 1996; pp 153-180.
-
(1996)
Advances in Knowledge Discovery and Data Mining
, pp. 153-180
-
-
Cheeseman, P.1
Stutz, J.2
-
58
-
-
36649006642
-
Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms
-
Shao, J. Y.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2312-2334
-
-
Shao, J.Y.1
Tanner, S.W.2
Thompson, N.3
Cheatham, T.E.4
-
59
-
-
84906257026
-
-
AutoClass C, version 3.3.6; (accessed Apr. 15).
-
Cook, D.; Potts, J.; Taylor, W. AutoClass C, version 3.3.6; http://ti.arc.nasa.gov/tech/rse/synthesis-projects-applications/autoclass/ autoclass-c/ (accessed Apr. 15, 2014).
-
(2014)
-
-
Cook, D.1
Potts, J.2
Taylor, W.3
-
60
-
-
66749085629
-
Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions
-
Huang, H.; Ozkirimli, E.; Post, C. B. Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions J. Chem. Theory Comput. 2009, 5, 1304-1314
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1304-1314
-
-
Huang, H.1
Ozkirimli, E.2
Post, C.B.3
-
61
-
-
84864247245
-
Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin
-
Ovchinnikov, V.; Karplus, M. Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin J. Phys. Chem. B 2012, 116, 8584-8603
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 8584-8603
-
-
Ovchinnikov, V.1
Karplus, M.2
-
62
-
-
0035876831
-
On the Bayesian approach to calculating time correlation functions in quantum systems; Reaction dynamics and spectroscopy
-
Krilov, G.; Sim, E.; Berne, B. J. On the Bayesian approach to calculating time correlation functions in quantum systems; reaction dynamics and spectroscopy Chem. Phys. 2001, 268, 21-34
-
(2001)
Chem. Phys.
, vol.268
, pp. 21-34
-
-
Krilov, G.1
Sim, E.2
Berne, B.J.3
-
63
-
-
18744387720
-
Reaction coordinates and rates from transition paths
-
Best, R. B.; Hummer, G. Reaction coordinates and rates from transition paths Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 6732-6737
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 6732-6737
-
-
Best, R.B.1
Hummer, G.2
-
64
-
-
57349094411
-
A Bayesian statistics approach to multiscale coarse graining
-
Liu, P.; Shi, Q.; Daume, H.; Voth, G. A. A Bayesian statistics approach to multiscale coarse graining J. Chem. Phys. 2008, 129 214114
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 214114
-
-
Liu, P.1
Shi, Q.2
Daume, H.3
Voth, G.A.4
-
65
-
-
33746878817
-
Bayesian model based clustering analysis: Application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core
-
Li, Y. Bayesian model based clustering analysis: Application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core J. Chem. Inf. Model. 2006, 46, 1742-1750
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 1742-1750
-
-
Li, Y.1
-
66
-
-
77149131242
-
Comparing geometric and kinetic cluster algorithms for molecular simulation data
-
Keller, B.; Daura, X.; van Gunsteren, W. F. Comparing geometric and kinetic cluster algorithms for molecular simulation data J. Chem. Phys. 2010, 132 074110
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 074110
-
-
Keller, B.1
Daura, X.2
Van Gunsteren, W.F.3
-
67
-
-
0034665713
-
Structural mechanism for STI-571 inhibition of Abelson tyrosine kinase
-
Schindler, T.; Bornmann, W.; Pellicena, P.; Miller, W. T.; Clarkson, B.; Kuriyan, J. Structural mechanism for STI-571 inhibition of Abelson tyrosine kinase Science 2000, 289, 1938-1942
-
(2000)
Science
, vol.289
, pp. 1938-1942
-
-
Schindler, T.1
Bornmann, W.2
Pellicena, P.3
Miller, W.T.4
Clarkson, B.5
Kuriyan, J.6
-
68
-
-
33745002702
-
An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
-
Zhang, X. W.; Gureasko, J.; Shen, K.; Cole, P. A.; Kuriyan, J. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor Cell 2006, 125, 1137-1149
-
(2006)
Cell
, vol.125
, pp. 1137-1149
-
-
Zhang, X.W.1
Gureasko, J.2
Shen, K.3
Cole, P.A.4
Kuriyan, J.5
-
69
-
-
0242268469
-
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
-
Miyashita, O.; Onuchic, J. N.; Wolynes, P. G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 12570-12575
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 12570-12575
-
-
Miyashita, O.1
Onuchic, J.N.2
Wolynes, P.G.3
-
70
-
-
33846847773
-
Conformational transitions of adenylate kinase: Switching by cracking
-
Whitford, P. C.; Miyashita, O.; Levy, Y.; Onuchic, J. N. Conformational transitions 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
-
71
-
-
62549167040
-
Ligand-induced global transitions in the catalytic domain of protein kinase A
-
Hyeon, C.; Jennings, P. A.; Adams, J. A.; Onuchic, J. N. Ligand-induced global transitions in the catalytic domain of protein kinase A Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 3023-3028
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 3023-3028
-
-
Hyeon, C.1
Jennings, P.A.2
Adams, J.A.3
Onuchic, J.N.4
-
72
-
-
84860870716
-
Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization
-
Shan, Y.; Eastwood, M. P.; Zhang, X.; Kim, E. T.; Arkhipov, A.; Dror, R. O.; Jumper, J.; Kuriyan, J.; Shaw, D. E. Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization Cell 2012, 149, 860-870
-
(2012)
Cell
, vol.149
, pp. 860-870
-
-
Shan, Y.1
Eastwood, M.P.2
Zhang, X.3
Kim, E.T.4
Arkhipov, A.5
Dror, R.O.6
Jumper, J.7
Kuriyan, J.8
Shaw, D.E.9
|