-
1
-
-
11844295361
-
Amyloidosis and Protein Folding
-
B. L. Kagan, "Amyloidosis and Protein Folding," Science 307, No. 5706, 42-43 (2005).
-
(2005)
Science
, vol.307
, Issue.5706
, pp. 42-43
-
-
Kagan, B.L.1
-
2
-
-
18244364614
-
-
J. Klein-Seetharaman, M. Oikawa, S. B. Grimshaw, J. Wirmer, E. Duchardt, T. Ueda, T. Imoto, L. J. Smith, C. M. Dobson, and H. Schwalbe, Long-Range Interactions Within a Nonnative Protein, Science 295, No. 5560, 1719-1722 (2002).
-
J. Klein-Seetharaman, M. Oikawa, S. B. Grimshaw, J. Wirmer, E. Duchardt, T. Ueda, T. Imoto, L. J. Smith, C. M. Dobson, and H. Schwalbe, "Long-Range Interactions Within a Nonnative Protein," Science 295, No. 5560, 1719-1722 (2002).
-
-
-
-
3
-
-
0042467574
-
A Camelid Antibody Fragment Inhibits the Formation of Amyloid Fibrils by Human Lysozyme
-
M. Dumoulin, A. Last, A. Desmyter, K. Decanniere, D. Canet, A. Spencer, D. Archer, et al., "A Camelid Antibody Fragment Inhibits the Formation of Amyloid Fibrils by Human Lysozyme," Nature 424, No. 6950, 783-788 (2003).
-
(2003)
Nature
, vol.424
, Issue.6950
, pp. 783-788
-
-
Dumoulin, M.1
Last, A.2
Desmyter, A.3
Decanniere, K.4
Canet, D.5
Spencer, A.6
Archer, D.7
-
4
-
-
0042467550
-
Rationalization of the Effects of Mutations on Peptide and Protein Aggregation Rates
-
F. Chiti, M. Stefani, N. Taddei, G. Ramponi, and C. M. Dobson, "Rationalization of the Effects of Mutations on Peptide and Protein Aggregation Rates," Nature 424, No. 6950, 805-808 (2003).
-
(2003)
Nature
, vol.424
, Issue.6950
, pp. 805-808
-
-
Chiti, F.1
Stefani, M.2
Taddei, N.3
Ramponi, G.4
Dobson, C.M.5
-
5
-
-
0025221747
-
Effect of Chemical Modifications of Tryptophan Residues on the Folding of Reduced Hen Egg-White Lysozyme
-
T. Ueda, H. Yamada, H. Aoki, and T. Imoto, "Effect of Chemical Modifications of Tryptophan Residues on the Folding of Reduced Hen Egg-White Lysozyme," J. Biochem. (Tokyo) 108, No. 5, 886-892 (1990).
-
(1990)
J. Biochem. (Tokyo)
, vol.108
, Issue.5
, pp. 886-892
-
-
Ueda, T.1
Yamada, H.2
Aoki, H.3
Imoto, T.4
-
6
-
-
33947658419
-
A Particular Hydrophobic Cluster in the Residual Structure of Reduced Lysozyme Drastically Affects the Amyloid Fibrils Formation
-
T. Mishima, T. Ohkuri, A. Monji, T. Imoto, and T. Ueda, "A Particular Hydrophobic Cluster in the Residual Structure of Reduced Lysozyme Drastically Affects the Amyloid Fibrils Formation," Biochem. Biophys. Res. Comm. 356, No. 3, 769-772 (2007).
-
(2007)
Biochem. Biophys. Res. Comm
, vol.356
, Issue.3
, pp. 769-772
-
-
Mishima, T.1
Ohkuri, T.2
Monji, A.3
Imoto, T.4
Ueda, T.5
-
7
-
-
0034958341
-
Blue Gene: A Vision for Protein Science Using a Petaflop Supercomputer
-
F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, et al., "Blue Gene: A Vision for Protein Science Using a Petaflop Supercomputer," IBM Syst. J. 40, No. 2, 310-327 (2001).
-
(2001)
IBM Syst. J
, vol.40
, Issue.2
, pp. 310-327
-
-
Allen, F.1
Almasi, G.2
Andreoni, W.3
Beece, D.4
Berne, B.J.5
Bright, A.6
Brunheroto, J.7
-
8
-
-
0037154980
-
Protein Folding and Unfolding at Atomic Resolution
-
A. R. Fersht and V. Daggett, "Protein Folding and Unfolding at Atomic Resolution," Cell 108, No. 4, 573-582 (2002).
-
(2002)
Cell
, vol.108
, Issue.4
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
9
-
-
0344301982
-
Protein Folding: A Perspective from Theory and Experiment
-
C. M. Dobson, A. Sali, and M. Karplus, "Protein Folding: A Perspective from Theory and Experiment," Angew Chem. Int. Edit. Engl. 37, 868-893 (1998).
-
(1998)
Angew Chem. Int. Edit. Engl
, vol.37
, pp. 868-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
10
-
-
0032530847
-
Chemical Physics of Protein Folding
-
C. L. Brooks, M. Gruebele, J. N. Onuchic, and P. G. Wolynes, "Chemical Physics of Protein Folding," Proc. Natl. Acad Sci. USA 95, No. 19, 11037-11038 (1998).
-
(1998)
Proc. Natl. Acad Sci. USA
, vol.95
, Issue.19
, pp. 11037-11038
-
-
Brooks, C.L.1
Gruebele, M.2
Onuchic, J.N.3
Wolynes, P.G.4
-
11
-
-
0032561237
-
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
-
Y. Duan and P. A. Kollman, "Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution," Science 282, No. 5389, 740-744 (1998).
-
(1998)
Science
, vol.282
, Issue.5389
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
12
-
-
4644236471
-
Hydrophobic Collapse in Multidomain Protein Folding
-
R. Zhou, X. Huang, C. J. Margulius, and B. J. Berne, "Hydrophobic Collapse in Multidomain Protein Folding," Science 305, No. 5690, 1605-1609 (2004).
-
(2004)
Science
, vol.305
, Issue.5690
, pp. 1605-1609
-
-
Zhou, R.1
Huang, X.2
Margulius, C.J.3
Berne, B.J.4
-
13
-
-
24344448662
-
Observation of a Dewetting Transition in the Collapse of the Melittin Tetramer
-
P. Liu, X. Huang, R. Zhou, and B. J. Berne, "Observation of a Dewetting Transition in the Collapse of the Melittin Tetramer," Nature 437, No. 7055, 159-162 (2005).
-
(2005)
Nature
, vol.437
, Issue.7055
, pp. 159-162
-
-
Liu, P.1
Huang, X.2
Zhou, R.3
Berne, B.J.4
-
14
-
-
0037038372
-
Absolute Comparison of Simulated and Experimental Protein-Folding Dynamics
-
C. D. Snow, H. Nguyen, V. S Pande, and M. Gruebele, "Absolute Comparison of Simulated and Experimental Protein-Folding Dynamics," Nature 420, No. 6911, 102-106 (2002).
-
(2002)
Nature
, vol.420
, Issue.6911
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
15
-
-
0034033187
-
Long Timescale Simulations
-
V. Daggett, "Long Timescale Simulations," Curr. Opin. Struct. Biol. 10, No. 2, 160-164 (2000).
-
(2000)
Curr. Opin. Struct. Biol
, vol.10
, Issue.2
, pp. 160-164
-
-
Daggett, V.1
-
16
-
-
0028929556
-
Principles of Protein Folding - A Perspective from Simple Exact Models
-
K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, "Principles of Protein Folding - A Perspective from Simple Exact Models," Protein Sci. 4, No. 4, 561-602 (1995).
-
(1995)
Protein Sci
, vol.4
, Issue.4
, pp. 561-602
-
-
Dill, K.A.1
Bromberg, S.2
Yue, K.3
Fiebig, K.M.4
Yee, D.P.5
Thomas, P.D.6
Chan, H.S.7
-
17
-
-
11244291006
-
Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model
-
F, Ding, S. V. Buldyrev, and N. V. Dokholyan, "Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model," Biophys. J. 88, No. 1, 147-155, (2005).
-
(2005)
Biophys. J
, vol.88
, Issue.1
, pp. 147-155
-
-
Ding, F.1
Buldyrev, S.V.2
Dokholyan, N.V.3
-
18
-
-
0029912748
-
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
-
W. L Jorgensen, D. Maxwell, and J. Tirado-Rives, "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids," J. Am. Chem. Soc. 118, No. 45, 11225-11236 (1996).
-
(1996)
J. Am. Chem. Soc
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.2
Tirado-Rives, J.3
-
19
-
-
0041784950
-
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, et al., "All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins," J. Phys. Chem. B 102, No. 18, 3586-3616 (1998).
-
(1998)
J. Phys. Chem. B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
-
20
-
-
33750060447
-
Thermal Denaturing of Mutant Lysozyme with Both the OPLSAA and the CHARMM Force Fields
-
M. Eleftheriou, R. S. Germain, A. K. Royyuru, and R. Zhou, "Thermal Denaturing of Mutant Lysozyme with Both the OPLSAA and the CHARMM Force Fields," J. Am. Chem. Soc. 128, No. 41, 13388-13395 (2006).
-
(2006)
J. Am. Chem. Soc
, vol.128
, Issue.41
, pp. 13388-13395
-
-
Eleftheriou, M.1
Germain, R.S.2
Royyuru, A.K.3
Zhou, R.4
-
21
-
-
0037381819
-
Simulations of Human Lysozyme: Probing the Conformations Triggering Amyloidosis
-
G. Moraitakis and J. M. Goodfellow, "Simulations of Human Lysozyme: Probing the Conformations Triggering Amyloidosis," Biophys. J. 84, No. 4, 2149-2158 (2003).
-
(2003)
Biophys. J
, vol.84
, Issue.4
, pp. 2149-2158
-
-
Moraitakis, G.1
Goodfellow, J.M.2
-
22
-
-
0032606076
-
-
C. Venclovas, A. Zenla, K. Fidelis, and J. Moult, Some Measures of Comparative Performance in the Three CASPs, Proteins S3, 231-237 (1999).
-
C. Venclovas, A. Zenla, K. Fidelis, and J. Moult, "Some Measures of Comparative Performance in the Three CASPs," Proteins S3, 231-237 (1999).
-
-
-
-
23
-
-
0344609869
-
Molecular Dynamics Simulations of the Hyperthermophilic Protein Sac7d from Sulfolobus acidocaldarius: Contribution of Salt Bridges to Thermostability
-
P. I. de Bakker, P. H. Hunenberger, and J. A. McCammon, "Molecular Dynamics Simulations of the Hyperthermophilic Protein Sac7d from Sulfolobus acidocaldarius: Contribution of Salt Bridges to Thermostability," J. Mol. Biol. 285, 1811-1830 (1999).
-
(1999)
J. Mol. Biol
, vol.285
, pp. 1811-1830
-
-
de Bakker, P.I.1
Hunenberger, P.H.2
McCammon, J.A.3
-
24
-
-
0029619259
-
Knowledge-Based Protein Secondary Structure Assignment
-
D. Frishman and P. Argos, "Knowledge-Based Protein Secondary Structure Assignment," Proteins 23, No. 4, 566-579 (1995).
-
(1995)
Proteins
, vol.23
, Issue.4
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
25
-
-
0037441479
-
Comparison of a QM/MM Force Field and Molecular Mechanics Force Fields in Simulations of Alanine and Glycine Dipeptides (Ace-Ala-Nine and Ace-Gly-Nme) in Water in Relation to the Problem of Modeling the Unfolded Peptide Backbone in Solution
-
H. Hu, M. Elstner, and J. Hermans, "Comparison of a QM/MM Force Field and Molecular Mechanics Force Fields in Simulations of Alanine and Glycine Dipeptides (Ace-Ala-Nine and Ace-Gly-Nme) in Water in Relation to the Problem of Modeling the Unfolded Peptide Backbone in Solution," Proteins 50, No. 3, 451-463 (2003).
-
(2003)
Proteins
, vol.50
, Issue.3
, pp. 451-463
-
-
Hu, H.1
Elstner, M.2
Hermans, J.3
-
26
-
-
0033529946
-
Understanding Beta-Hairpin Formation
-
A. R. Dinner, T. Lazaridis, and M. Karplus, "Understanding Beta-Hairpin Formation," Proc. Natl. Acad. Sci. USA 96, No. 16, 9068-9073 (1999).
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, Issue.16
, pp. 9068-9073
-
-
Dinner, A.R.1
Lazaridis, T.2
Karplus, M.3
-
27
-
-
0035909921
-
The Free Energy Landscape for Beta-Hairpin Folding in Explicit Water
-
R. Zhou B. J. Berne, and R. S. Germain, "The Free Energy Landscape for Beta-Hairpin Folding in Explicit Water," Proc. Natl. Acad. Sci. USA 98, No. 26, 14931-14936 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, Issue.26
, pp. 14931-14936
-
-
Zhou, R.1
Berne, B.J.2
Germain, R.S.3
-
28
-
-
34347219018
-
-
R. Zhou, M. Eleftheriou, A. Royyuru, and B. J. Berne, Destruction of Long-Range Interactions by a Single Mutation in Lysozyme, Proc. Natl. Acad. Sci. USA 104, No. 14, 5824-5829 (2007).
-
R. Zhou, M. Eleftheriou, A. Royyuru, and B. J. Berne, Destruction of Long-Range Interactions by a Single Mutation in Lysozyme," Proc. Natl. Acad. Sci. USA 104, No. 14, 5824-5829 (2007).
-
-
-
-
29
-
-
0033578302
-
Cation - Pi Interactions in Structural Biology
-
J. P. Gallivan and D. A. Dougherty, "Cation - Pi Interactions in Structural Biology," Proc. Natl. Acad. Sci. USA 96, No. 17, 9459-9464 (1999).
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, Issue.17
, pp. 9459-9464
-
-
Gallivan, J.P.1
Dougherty, D.A.2
-
30
-
-
0028351165
-
Contribution of Unusual Arginine - Arginine Short-Range Interactions to Stabilization and Recognition in Proteins
-
A. Magalhaes, B. Maigret, J. Hoflack, J. N. Gomes, and H. A. Scheraga, "Contribution of Unusual Arginine - Arginine Short-Range Interactions to Stabilization and Recognition in Proteins," J. Protein Chem. 13, No. 2, 195-215 (1994).
-
(1994)
J. Protein Chem
, vol.13
, Issue.2
, pp. 195-215
-
-
Magalhaes, A.1
Maigret, B.2
Hoflack, J.3
Gomes, J.N.4
Scheraga, H.A.5
-
31
-
-
0002775934
-
Interaction Models for Water in Relation to Protein Hydration
-
B. Pullman, Ed, Reidel, Dordrecht
-
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Herman, "Interaction Models for Water in Relation to Protein Hydration," Intermolecular Forces, B. Pullman, Ed., Reidel, Dordrecht, 1981, pp. 331-342.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Herman, J.4
-
32
-
-
0000036869
-
Simulation of Activation Free Energies in Molecular Systems
-
E. Neria, S. Fischer, and M. Karplus, "Simulation of Activation Free Energies in Molecular Systems," J. Chem. Phys. 105, No. 5, 1902-1921 (1996).
-
(1996)
J. Chem. Phys
, vol.105
, Issue.5
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
33
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
W. L. Jorgensen, J. Chandrasekhar, J. Madura, R. W. Impey, and M. L. Klein, "Comparison of Simple Potential Functions for Simulating Liquid Water," J. Chem. Phys. 79, No. 2, 926-935 (1983).
-
(1983)
J. Chem. Phys
, vol.79
, Issue.2
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.W.4
Klein, M.L.5
-
34
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
U. Essman, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, "A Smooth Particle Mesh Ewald Method," J. Chem. Phys. 103, No. 19, 8577-8593 (1995).
-
(1995)
J. Chem. Phys
, vol.103
, Issue.19
, pp. 8577-8593
-
-
Essman, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
35
-
-
0142010565
-
Blue Matter, an Application Framework for Molecular Simulation on Blue Gene
-
B. G. Fitch, R. S. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, et al., "Blue Matter, an Application Framework for Molecular Simulation on Blue Gene," J. Parallel Distrib. Comput. 63, No. 7-8, 759-773 (2003).
-
(2003)
J. Parallel Distrib. Comput
, vol.63
, Issue.7-8
, pp. 759-773
-
-
Fitch, B.G.1
Germain, R.S.2
Mendell, M.3
Pitera, J.4
Pitman, M.5
Rayshubskiy, A.6
Sham, Y.7
-
36
-
-
0033134665
-
Structural Details of Urea Binding to Barnase: A Molecular Dynamics Analysis
-
A. Caflisch and M. Karplus, "Structural Details of Urea Binding to Barnase: A Molecular Dynamics Analysis," Structure 7, No. 5, 477-488 (1999).
-
(1999)
Structure
, vol.7
, Issue.5
, pp. 477-488
-
-
Caflisch, A.1
Karplus, M.2
-
37
-
-
27344436659
-
Scalable Molecular Dynamics with. NAMD
-
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten, "Scalable Molecular Dynamics with. NAMD," J. Comput. Chem. 26, No. 16, 1781-1802 (2005).
-
(2005)
J. Comput. Chem
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
|