-
1
-
-
0347987853
-
Folding proteins in fatal ways
-
Selkoe DJ. Folding proteins in fatal ways. Nature 2003;426:900-904.
-
(2003)
Nature
, vol.426
, pp. 900-904
-
-
Selkoe, D.J.1
-
2
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006;75:333-366.
-
(2006)
Annu Rev Biochem
, vol.75
, pp. 333-366
-
-
Chiti, F.1
Dobson, C.M.2
-
4
-
-
0242668337
-
Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
-
Kayed R, Head E, Thompson JL, McIntire TM, Milton SC, Cotman CW, Glabe CG. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 2003;300:486-489.
-
(2003)
Science
, vol.300
, pp. 486-489
-
-
Kayed, R.1
Head, E.2
Thompson, J.L.3
McIntire, T.M.4
Milton, S.C.5
Cotman, C.W.6
Glabe, C.G.7
-
5
-
-
0037397705
-
Emerging ideas on the molecular basis of protein and peptide aggregation
-
Thirumalai D, Klimov DK, Dima RI. Emerging ideas on the molecular basis of protein and peptide aggregation. Curr Opin Struct Biol 2003;13:146-159.
-
(2003)
Curr Opin Struct Biol
, vol.13
, pp. 146-159
-
-
Thirumalai, D.1
Klimov, D.K.2
Dima, R.I.3
-
6
-
-
0037041426
-
Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo
-
Walsh DM, Klyubin I, Fadeeva JV, Cullen WK, Anwyl R, Wolfe MS, Rowan MJ, Selkoe DJ. Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo. Nature 2002;416:535-539.
-
(2002)
Nature
, vol.416
, pp. 535-539
-
-
Walsh, D.M.1
Klyubin, I.2
Fadeeva, J.V.3
Cullen, W.K.4
Anwyl, R.5
Wolfe, M.S.6
Rowan, M.J.7
Selkoe, D.J.8
-
7
-
-
0036708168
-
Paradigm shifts in Alzheimers disease and other neurodegenerative disorders: the emerging role of oligomeric assemblies
-
Kirkitadze MD, Bitan G, Teplow DB. Paradigm shifts in Alzheimers disease and other neurodegenerative disorders: the emerging role of oligomeric assemblies. J Neurosci Res 2002;69:567-577.
-
(2002)
J Neurosci Res
, vol.69
, pp. 567-577
-
-
Kirkitadze, M.D.1
Bitan, G.2
Teplow, D.B.3
-
8
-
-
0037041420
-
Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases
-
Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 2002;416:507-511.
-
(2002)
Nature
, vol.416
, pp. 507-511
-
-
Bucciantini, M.1
Giannoni, E.2
Chiti, F.3
Baroni, F.4
Formigli, L.5
Zurdo, J.6
Taddei, N.7
Ramponi, G.8
Dobson, C.M.9
Stefani, M.10
-
9
-
-
2542455537
-
Small assemblies of unmodied amyloid β-protein are the proximate neurotoxin in Alzheimers disease
-
Klein WL, Stine WB, Teplow DB. Small assemblies of unmodied amyloid β-protein are the proximate neurotoxin in Alzheimers disease. Neurobiol Aging 2004;25:569-580.
-
(2004)
Neurobiol Aging
, vol.25
, pp. 569-580
-
-
Klein, W.L.1
Stine, W.B.2
Teplow, D.B.3
-
10
-
-
0035956924
-
An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid
-
Balbirnie M, Grothe R, Eisenberg DS. An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid. Proc Natl Acad Sci USA 2001;98:2375-2380.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 2375-2380
-
-
Balbirnie, M.1
Grothe, R.2
Eisenberg, D.S.3
-
11
-
-
20444440728
-
Structure of the cross-β spine of amyloid-like fibrils
-
Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, Grothe R, Eisenberg D. Structure of the cross-β spine of amyloid-like fibrils. Nature 2005;435:773-778.
-
(2005)
Nature
, vol.435
, pp. 773-778
-
-
Nelson, R.1
Sawaya, M.R.2
Balbirnie, M.3
Madsen, A.4
Riekel, C.5
Grothe, R.6
Eisenberg, D.7
-
12
-
-
34249290108
-
Atomic structures of amyloid cross-beta; spines reveal varied steric zippers
-
Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJ, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. Atomic structures of amyloid cross-beta; spines reveal varied steric zippers. Nature 2007;447:453-457.
-
(2007)
Nature
, vol.447
, pp. 453-457
-
-
Sawaya, M.R.1
Sambashivan, S.2
Nelson, R.3
Ivanova, M.I.4
Sievers, S.A.5
Apostol, M.I.6
Thompson, M.J.7
Balbirnie, M.8
Wiltzius, J.J.9
McFarlane, H.T.10
Madsen, A.11
Riekel, C.12
Eisenberg, D.13
-
13
-
-
78149340576
-
Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR
-
van der Wel PCA, Lewandowski JR, Griffin RG. Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR. Biochemistry 2010;49:9457-9469.
-
(2010)
Biochemistry
, vol.49
, pp. 9457-9469
-
-
van der Wel, P.C.A.1
Lewandowski, J.R.2
Griffin, R.G.3
-
14
-
-
33750017513
-
Molecular structure of amyloid fibrils: insights from solid-state NMR
-
Tycko R. Molecular structure of amyloid fibrils: insights from solid-state NMR. Q Rev Biophys 2006;39:1-55.
-
(2006)
Q Rev Biophys
, vol.39
, pp. 1-55
-
-
Tycko, R.1
-
15
-
-
38849108169
-
Solid-state NMR spectroscopy of amyloid proteins
-
Heise H. Solid-state NMR spectroscopy of amyloid proteins. ChemBioChem 2008;9:179-189.
-
(2008)
ChemBioChem
, vol.9
, pp. 179-189
-
-
Heise, H.1
-
17
-
-
0037627715
-
The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
-
Gsponer J, Haberthür U, Caflisch A. The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc Natl Acad Sci USA 2003;100:5154-5159.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5154-5159
-
-
Gsponer, J.1
Haberthür, U.2
Caflisch, A.3
-
18
-
-
10844230140
-
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
-
Cecchini M, Rao F, Seeber M, Caflisch A. Replica exchange molecular dynamics simulations of amyloid peptide aggregation. J Chem Phys 2004;121:10748.
-
(2004)
J Chem Phys
, vol.121
, pp. 10748
-
-
Cecchini, M.1
Rao, F.2
Seeber, M.3
Caflisch, A.4
-
19
-
-
19444380574
-
Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing
-
Lipfert J, Franklin J, Wu F, Doniach S. Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing. J Mol Biol 2005;349:648-658.
-
(2005)
J Mol Biol
, vol.349
, pp. 648-658
-
-
Lipfert, J.1
Franklin, J.2
Wu, F.3
Doniach, S.4
-
20
-
-
33746765060
-
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion Sup-35
-
Zheng J, Ma B, Tsai CJ, Nussinov R. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion Sup-35. Biophys J 2006;91:824-833.
-
(2006)
Biophys J
, vol.91
, pp. 824-833
-
-
Zheng, J.1
Ma, B.2
Tsai, C.J.3
Nussinov, R.4
-
21
-
-
33746800825
-
Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation
-
Esposito L, Pedone C, Vitagliano L. Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation. Proc Natl Acad Sci USA 2006;103:11533-11538.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 11533-11538
-
-
Esposito, L.1
Pedone, C.2
Vitagliano, L.3
-
22
-
-
34548627237
-
Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35
-
Zhang Z, Chen H, Bai H, Lai L. Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35. Biophys J 2007;93:1484-1492.
-
(2007)
Biophys J
, vol.93
, pp. 1484-1492
-
-
Zhang, Z.1
Chen, H.2
Bai, H.3
Lai, L.4
-
23
-
-
37549055108
-
Thermodynamics and kinetics of aggregation for the GNNQQNY peptide
-
Strodel B, Whittleston CS, Wales DJ. Thermodynamics and kinetics of aggregation for the GNNQQNY peptide. J Am Chem Soc 2007;129:16005-16014.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 16005-16014
-
-
Strodel, B.1
Whittleston, C.S.2
Wales, D.J.3
-
24
-
-
58149360794
-
All-atom computer simulations of amyloid fibrils disaggregation
-
Wang J, Tan C, Chen HF, Luo R. All-atom computer simulations of amyloid fibrils disaggregation. Biophys J 2008;95:5037-5047.
-
(2008)
Biophys J
, vol.95
, pp. 5037-5047
-
-
Wang, J.1
Tan, C.2
Chen, H.F.3
Luo, R.4
-
25
-
-
44849096158
-
Investigating the mechanism of peptide aggregation: insights from mixed Monte Carlo-molecular dynamics simulations
-
Meli M, Morra G, Colombo G. Investigating the mechanism of peptide aggregation: insights from mixed Monte Carlo-molecular dynamics simulations. Biophys J 2008;94:4414-4426.
-
(2008)
Biophys J
, vol.94
, pp. 4414-4426
-
-
Meli, M.1
Morra, G.2
Colombo, G.3
-
26
-
-
56349091416
-
Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association
-
Vitagliano L, Esposito L, Pedone C, de Simone A. Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association. Biochem Biophys Res Commun 2008;377:1036-1041.
-
(2008)
Biochem Biophys Res Commun
, vol.377
, pp. 1036-1041
-
-
Vitagliano, L.1
Esposito, L.2
Pedone, C.3
de Simone, A.4
-
27
-
-
70349658765
-
Thermodynamic selection of steric zipper patterns in the amyloid cross-β spine
-
Park J, Kahng B, Hwang W. Thermodynamic selection of steric zipper patterns in the amyloid cross-β spine. PLoS Comput Biol 2009;5:e1000492.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Park, J.1
Kahng, B.2
Hwang, W.3
-
28
-
-
68849107584
-
Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation
-
Berryman JT, Radford SE, Harris SA. Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation. Biophys J 2009;97:1-11.
-
(2009)
Biophys J
, vol.97
, pp. 1-11
-
-
Berryman, J.T.1
Radford, S.E.2
Harris, S.A.3
-
29
-
-
61949163833
-
Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide
-
Periole X, Rampioni A, Vendruscolo M, Mark AE. Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide. J Phys Chem B 2009;113:1728-1737.
-
(2009)
J Phys Chem B
, vol.113
, pp. 1728-1737
-
-
Periole, X.1
Rampioni, A.2
Vendruscolo, M.3
Mark, A.E.4
-
30
-
-
77949612059
-
GNNQQNY-investigation of early steps during amyloid formation
-
Reddy AS, Chopra M, de Pablo JJ. GNNQQNY-investigation of early steps during amyloid formation. Biophys J 2010;98:1038-1045.
-
(2010)
Biophys J
, vol.98
, pp. 1038-1045
-
-
Reddy, A.S.1
Chopra, M.2
de Pablo, J.J.3
-
31
-
-
79958122197
-
A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35
-
Nasica-Labouze J, Meli M, Derreumaux P, Colombo G, Mousseau N. A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35. PLoS Comput Biol 2011;7:e1002051.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Nasica-Labouze, J.1
Meli, M.2
Derreumaux, P.3
Colombo, G.4
Mousseau, N.5
-
32
-
-
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
-
33
-
-
79953081933
-
Coarse-grained models for protein aggregation
-
Wu C, Shea JE. Coarse-grained models for protein aggregation. Curr Opin Struct Biol 2011;21:209-220.
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 209-220
-
-
Wu, C.1
Shea, J.E.2
-
34
-
-
33745727173
-
Interpreting the aggregation kinetics of amyloid peptides
-
Pellarin R, Caflisch A. Interpreting the aggregation kinetics of amyloid peptides. J Mol Biol 2006;360:882-892.
-
(2006)
J Mol Biol
, vol.360
, pp. 882-892
-
-
Pellarin, R.1
Caflisch, A.2
-
35
-
-
35748943830
-
Pathways and intermediates of amyloid fibril formation
-
Pellarin R, Guarnera E, Caflisch A. Pathways and intermediates of amyloid fibril formation. J Mol Biol 2007;374:917-924.
-
(2007)
J Mol Biol
, vol.374
, pp. 917-924
-
-
Pellarin, R.1
Guarnera, E.2
Caflisch, A.3
-
36
-
-
77958510689
-
Crowding effects on amyloid aggregation kinetics
-
Magno A, Caflisch A, Pellarin R. Crowding effects on amyloid aggregation kinetics. J Phys Chem Lett 2010;1:3027-3032.
-
(2010)
J Phys Chem Lett
, vol.1
, pp. 3027-3032
-
-
Magno, A.1
Caflisch, A.2
Pellarin, R.3
-
37
-
-
34547251863
-
Self-assembly of β-sheet forming peptides into chiral fibrillar clusters
-
Bellesia G, Shea JE. Self-assembly of β-sheet forming peptides into chiral fibrillar clusters. J Chem Phys 2007;126:245104.
-
(2007)
J Chem Phys
, vol.126
, pp. 245104
-
-
Bellesia, G.1
Shea, J.E.2
-
38
-
-
52049104642
-
Structure and stability of amyloid fibrils formed from synthetic β-peptides
-
Bellesia G, Shea JE. Structure and stability of amyloid fibrils formed from synthetic β-peptides. Front Biosci 2008;13:6957-6965.
-
(2008)
Front Biosci
, vol.13
, pp. 6957-6965
-
-
Bellesia, G.1
Shea, J.E.2
-
39
-
-
65249190783
-
Effect of β-sheet propensity on peptide aggregation
-
Bellesia G, Shea JE. Effect of β-sheet propensity on peptide aggregation. J Chem Phys 2009;130:145103.
-
(2009)
J Chem Phys
, vol.130
, pp. 145103
-
-
Bellesia, G.1
Shea, J.E.2
-
40
-
-
72949120775
-
Diversity of kinetic pathways in amyloid fibril formation
-
Bellesia G, Shea JE. Diversity of kinetic pathways in amyloid fibril formation. J Chem Phys 2009;131:111102.
-
(2009)
J Chem Phys
, vol.131
, pp. 111102
-
-
Bellesia, G.1
Shea, J.E.2
-
41
-
-
9244260521
-
Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
-
Nguyen HD, Hall CK. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc Natl Acad Sci USA 2004;101:16180-16185.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 16180-16185
-
-
Nguyen, H.D.1
Hall, C.K.2
-
42
-
-
33244456166
-
Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations
-
Nguyen HD, Hall CK. Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations. J Am Chem Soc 2006;128:1890-1901.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 1890-1901
-
-
Nguyen, H.D.1
Hall, C.K.2
-
43
-
-
77957965654
-
Extending the PRIME model for protein aggregation to all 20 amino acids
-
Cheon M, Chang I, Hall CK. Extending the PRIME model for protein aggregation to all 20 amino acids. Proteins: Struct Funct Bioinf 2010;78:2950-2960.
-
(2010)
Proteins: Struct Funct Bioinf
, vol.78
, pp. 2950-2960
-
-
Cheon, M.1
Chang, I.2
Hall, C.K.3
-
44
-
-
10644242867
-
Molecular dynamics simulation of amyloid β dimer formation
-
Urbanc B, Cruz L, Ding F, Sammond D, Khare S, Buldyrev SV, Stanley HE, Dokholyan NV. Molecular dynamics simulation of amyloid β dimer formation. Biophys J 2004;87:2310-2321.
-
(2004)
Biophys J
, vol.87
, pp. 2310-2321
-
-
Urbanc, B.1
Cruz, L.2
Ding, F.3
Sammond, D.4
Khare, S.5
Buldyrev, S.V.6
Stanley, H.E.7
Dokholyan, N.V.8
-
45
-
-
10644278760
-
In silico study of amyloid β-protein folding and oligomerization
-
Urbanc B, Cruz L, Yun S., Buldyrev SV, Bitan G, Teplow DB, Stanley HE. In silico study of amyloid β-protein folding and oligomerization. Proc Natl Acad Sci USA 2004;101:17345-17350.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 17345-17350
-
-
Urbanc, B.1
Cruz, L.2
Yun, S.3
Buldyrev, S.V.4
Bitan, G.5
Teplow, D.B.6
Stanley, H.E.7
-
46
-
-
77950219248
-
Elucidation of amyloid β-protein oligomerization mechanisms: discrete molecular dynamics study
-
Urbanc B, Betnel M, Cruz L, Bitan G, Teplow DB. Elucidation of amyloid β-protein oligomerization mechanisms: discrete molecular dynamics study. J Am Chem Soc 2010;132:4266-4280.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 4266-4280
-
-
Urbanc, B.1
Betnel, M.2
Cruz, L.3
Bitan, G.4
Teplow, D.B.5
-
47
-
-
0001418816
-
From polypeptide sequences to structures using Monte-Carlo simulations and an optimized potential
-
Derreumaux P. From polypeptide sequences to structures using Monte-Carlo simulations and an optimized potential. J Chem Phys 1999;111:2301-2310.
-
(1999)
J Chem Phys
, vol.111
, pp. 2301-2310
-
-
Derreumaux, P.1
-
48
-
-
34548067360
-
Following the aggregation of amyloid-forming peptides by computer simulations
-
Melquiond A, Boucher G, Mousseau N, Derreumaux P. Following the aggregation of amyloid-forming peptides by computer simulations. J Chem Phys 2005;122:174904.
-
(2005)
J Chem Phys
, vol.122
, pp. 174904
-
-
Melquiond, A.1
Boucher, G.2
Mousseau, N.3
Derreumaux, P.4
-
49
-
-
33846234246
-
Coarse-grained protein molecular dynamics simulations
-
Derreumaux P, Mousseau N. Coarse-grained protein molecular dynamics simulations. J Chem Phys 2007;126:025101.
-
(2007)
J Chem Phys
, vol.126
, pp. 025101
-
-
Derreumaux, P.1
Mousseau, N.2
-
50
-
-
34548809141
-
A coarse-grained protein force field for folding and structure prediction
-
Maupetit J, Tuffery P, Derreumaux P. A coarse-grained protein force field for folding and structure prediction. Proteins: Struct Funct Bioinf 2007;69:394-408.
-
(2007)
Proteins: Struct Funct Bioinf
, vol.69
, pp. 394-408
-
-
Maupetit, J.1
Tuffery, P.2
Derreumaux, P.3
-
51
-
-
67649101377
-
Generic coarse-grained model for protein folding and aggregation
-
Bereau T, Deserno M. Generic coarse-grained model for protein folding and aggregation. J Chem Phys 2009;130:235106.
-
(2009)
J Chem Phys
, vol.130
, pp. 235106
-
-
Bereau, T.1
Deserno, M.2
-
52
-
-
77957118527
-
Interplay between secondary and tertiary structure formation in protein folding cooperativity
-
Bereau T, Bachmann M, Deserno M. Interplay between secondary and tertiary structure formation in protein folding cooperativity. J Am Chem Soc 2010;132:13129-13131.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 13129-13131
-
-
Bereau, T.1
Bachmann, M.2
Deserno, M.3
-
53
-
-
79960312873
-
Structural basis of folding cooperativity in model proteins: insights from a microcanonical perspective
-
Bereau T, Deserno M, Bachmann M. Structural basis of folding cooperativity in model proteins: insights from a microcanonical perspective. Biophys J 2011;100:2764-2772.
-
(2011)
Biophys J
, vol.100
, pp. 2764-2772
-
-
Bereau, T.1
Deserno, M.2
Bachmann, M.3
-
54
-
-
84867351991
-
Coarse-grained and atomistic simulations of the salt-stable cowpea chlorotic mottle virus (ss-ccmv) subunit 2649: β-barrel stability of the hexamer and pentamer geometries
-
Bereau T, Globisch C, Deserno M, Peter C. Coarse-grained and atomistic simulations of the salt-stable cowpea chlorotic mottle virus (ss-ccmv) subunit 2649: β-barrel stability of the hexamer and pentamer geometries. J Chem Theory Comput 2012;8:3750-3758.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 3750-3758
-
-
Bereau, T.1
Globisch, C.2
Deserno, M.3
Peter, C.4
-
55
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996;256:623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
56
-
-
49449113010
-
The MARTINI coarse grained force field: extension to proteins
-
Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ. The MARTINI coarse grained force field: extension to proteins. J Chem Theor Comput 2008;4:819-834.
-
(2008)
J Chem Theor Comput
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.J.6
-
57
-
-
33645981294
-
ESPResSo-an extensible simulation package for research on soft matter systems
-
Limbach HJ, Arnold A, Mann BA, Holm C. ESPResSo-an extensible simulation package for research on soft matter systems. Comput Phys Commun 2006;174:704-727.
-
(2006)
Comput Phys Commun
, vol.174
, pp. 704-727
-
-
Limbach, H.J.1
Arnold, A.2
Mann, B.A.3
Holm, C.4
-
58
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys 1953;21:1087.
-
(1953)
J Chem Phys
, vol.21
, pp. 1087
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
59
-
-
67650140666
-
Optimized convergence for multiple histogram analysis
-
Bereau T, Swendsen RH. Optimized convergence for multiple histogram analysis. J Comput Phys 2009;228:6119-6129.
-
(2009)
J Comput Phys
, vol.228
, pp. 6119-6129
-
-
Bereau, T.1
Swendsen, R.H.2
-
60
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. 1: the method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. The weighted histogram analysis method for free-energy calculations on biomolecules. 1: the method. J Comput Chem 1992;13:1011-1021.
-
(1992)
J Comput Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
62
-
-
84927480293
-
Monte Carlo study of the isotropic and nematic phases of infinitely thin hard platelets
-
Eppenga R, Frenkel D. Monte Carlo study of the isotropic and nematic phases of infinitely thin hard platelets. Mol Phys 1984;52: 6:1303-1334.
-
(1984)
Mol Phys
, vol.52
, Issue.6
, pp. 1303-1334
-
-
Eppenga, R.1
Frenkel, D.2
-
63
-
-
67650403403
-
Amyloid protofibrils of lysozyme nucleate and grow via oligomer fusion
-
Hill SE, Robinson J, Matthews G, Muschol M. Amyloid protofibrils of lysozyme nucleate and grow via oligomer fusion. Biophys J 2009;96:3781-3790.
-
(2009)
Biophys J
, vol.96
, pp. 3781-3790
-
-
Hill, S.E.1
Robinson, J.2
Matthews, G.3
Muschol, M.4
-
64
-
-
84863971692
-
Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations
-
Lu Y, Wei G, Derreumaux P.Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations. J Chem Phys 2012;137:025101.
-
(2012)
J Chem Phys
, vol.137
, pp. 025101
-
-
Lu, Y.1
Wei, G.2
Derreumaux, P.3
-
65
-
-
58149174069
-
Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment
-
Li DW, Mohanty S, Irbäck A, Huo S. Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment. PLoS Comput Biol 2008;4:e1000238.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Li, D.W.1
Mohanty, S.2
Irbäck, A.3
Huo, S.4
-
66
-
-
33744807442
-
Sequence and structure analysis of parallel helices: implication for constructing amyloid structural models
-
Tsai HH, Gunasekaran K, Nussinov R. Sequence and structure analysis of parallel helices: implication for constructing amyloid structural models. Structure 2006;14:1059-1072.
-
(2006)
Structure
, vol.14
, pp. 1059-1072
-
-
Tsai, H.H.1
Gunasekaran, K.2
Nussinov, R.3
-
67
-
-
33845978790
-
Insight into the structure of amyloid fibrils from the analysis of globular proteins
-
Trovato A, Chiti F, Maritan A, Seno F. Insight into the structure of amyloid fibrils from the analysis of globular proteins. PLoS Comput Biol 2006;2:e170.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Trovato, A.1
Chiti, F.2
Maritan, A.3
Seno, F.4
-
68
-
-
84986512474
-
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
69
-
-
50549095455
-
Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide
-
Strodel B, Wales DJ. Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide. J Chem Theory Comput 2008;4:657-672.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 657-672
-
-
Strodel, B.1
Wales, D.J.2
-
70
-
-
79958770752
-
Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides
-
Wagoner VA, Cheon M, Chang I, Hall CK. Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides. Proteins: Struct Funct Bioinf 2011;79:2132-2145.
-
(2011)
Proteins: Struct Funct Bioinf
, vol.79
, pp. 2132-2145
-
-
Wagoner, V.A.1
Cheon, M.2
Chang, I.3
Hall, C.K.4
-
71
-
-
57149102288
-
A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates
-
Auer S, Meersman F, Dobson CM, Vendruscolo M. A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates. PLoS Comput Biol 2008;4:e1000222.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Auer, S.1
Meersman, F.2
Dobson, C.M.3
Vendruscolo, M.4
|