-
1
-
-
48749148224
-
Rattle - A velocity version of the shake algorithm for molecular-dynamics calculations
-
Andersen HC. 1983. Rattle-A velocity version of the shake algorithm for molecular-dynamics calculations. J Comp Phys 52(1):24-34.
-
(1983)
J Comp Phys
, vol.52
, Issue.1
, pp. 24-34
-
-
Andersen, H.C.1
-
2
-
-
0035151879
-
Competition between protein folding and aggregation: A three-dimensional lattice-model simulation
-
Bratko D, Blanch HW. 2001. Competition between protein folding and aggregation: A three-dimensional lattice-model simulation. J Chem Phys 114(1):561-569.
-
(2001)
J Chem Phys
, vol.114
, Issue.1
, pp. 561-569
-
-
Bratko, D.1
Blanch, H.W.2
-
3
-
-
0037444764
-
Effect of secondary structure on protein aggregation: A replica exchange simulation study
-
Bratko D, Blanch HW. 2003. Effect of secondary structure on protein aggregation: A replica exchange simulation study. J Chem Phys 118(11): 5185-5194.
-
(2003)
J Chem Phys
, vol.118
, Issue.11
, pp. 5185-5194
-
-
Bratko, D.1
Blanch, H.W.2
-
5
-
-
0032573090
-
Folding and aggregation of designed proteins
-
Broglia RA, Tiana G, Pasquali S, Roman HE, Vigezzi E. 1998. Folding and aggregation of designed proteins. Proc Natl Acad Sci USA 95(22): 12930-12933.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.22
, pp. 12930-12933
-
-
Broglia, R.A.1
Tiana, G.2
Pasquali, S.3
Roman, H.E.4
Vigezzi, E.5
-
6
-
-
0036166319
-
Kinetic partitioning of protein folding and aggregation
-
Chiti F, Taddei N, Baroni F, Capanni C, Stefani M, Ramponi G, Dobson C. 2002. Kinetic partitioning of protein folding and aggregation. Nature Struct Biol 9(2):137-143.
-
(2002)
Nature Struct Biol
, vol.9
, Issue.2
, pp. 137-143
-
-
Chiti, F.1
Taddei, N.2
Baroni, F.3
Capanni, C.4
Stefani, M.5
Ramponi, G.6
Dobson, C.7
-
7
-
-
0033616575
-
Designing conditions for in vitro formation of amyloid proto-filaments and fibrils
-
Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson C. 1999. Designing conditions for in vitro formation of amyloid proto-filaments and fibrils. Proc Natl Acad Sci USA 96:3590-3594.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3590-3594
-
-
Chiti, F.1
Webster, P.2
Taddei, N.3
Clark, A.4
Stefani, M.5
Ramponi, G.6
Dobson, C.7
-
8
-
-
0035313135
-
Protein refolding for industrial processes
-
Clark ED. 2001. Protein refolding for industrial processes. Curr Opin Biotechnol 12(2):202-207.
-
(2001)
Curr Opin Biotechnol
, vol.12
, Issue.2
, pp. 202-207
-
-
Clark, E.D.1
-
9
-
-
0036228167
-
Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics
-
Dima RI, Thirumalai D. 2002. Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics. Protein Sci 11(5):1036-1049.
-
(2002)
Protein Sci
, vol.11
, Issue.5
, pp. 1036-1049
-
-
Dima, R.I.1
Thirumalai, D.2
-
10
-
-
0035961329
-
The structural basis of protein folding and its links with human disease
-
Dobson C. 2001. The structural basis of protein folding and its links with human disease. Phil Trans R Soc London B 356:133-145.
-
(2001)
Phil Trans R Soc London B
, vol.356
, pp. 133-145
-
-
Dobson, C.1
-
11
-
-
0346734137
-
Myoglobin forms amyloid fibrils by association of unfolded polypeptide segments
-
Fandrich M, Forge V, Buder K, Kittler M, Dobson CM, Diekmann S. 2003. Myoglobin forms amyloid fibrils by association of unfolded polypeptide segments. Proc Natl Acad Sci USA 100(26):15463-15468.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.26
, pp. 15463-15468
-
-
Fandrich, M.1
Forge, V.2
Buder, K.3
Kittler, M.4
Dobson, C.M.5
Diekmann, S.6
-
12
-
-
0031932169
-
Protein aggregation: Folding aggregates, inclusion bodies, and amyloid
-
Fink A. 1998. Protein aggregation: Folding aggregates, inclusion bodies, and amyloid. Folding and Design 3:R9-R23.
-
(1998)
Folding and Design
, vol.3
-
-
Fink, A.1
-
13
-
-
0034275017
-
Compactness, aggregation, and prionlike behavior of protein: A lattice model study
-
Giugliarelli G, Micheletti C, Banavar JM, Maritan A. 2000. Compactness, aggregation, and prionlike behavior of protein: A lattice model study. J Chem Phys 113:5072-5077.
-
(2000)
J Chem Phys
, vol.113
, pp. 5072-5077
-
-
Giugliarelli, G.1
Micheletti, C.2
Banavar, J.M.3
Maritan, A.4
-
14
-
-
0037108179
-
Conformational prerequisites for alpha-lactalbumin fibrillation
-
Goers J, Permyakov SE, Permyakov EA, Uversky VN, Fink AL. 2002. Conformational prerequisites for alpha-lactalbumin fibrillation. Biochemistry 41(41): 12546-12551.
-
(2002)
Biochemistry
, vol.41
, Issue.41
, pp. 12546-12551
-
-
Goers, J.1
Permyakov, S.E.2
Permyakov, E.A.3
Uversky, V.N.4
Fink, A.L.5
-
15
-
-
0029010695
-
Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
-
Guo Z, Thirumalai D. 1995. Kinetics of protein folding: Nucleation mechanism, time scales, and pathways. Biopolymers 36:83-102.
-
(1995)
Biopolymers
, vol.36
, pp. 83-102
-
-
Guo, Z.1
Thirumalai, D.2
-
16
-
-
0002689652
-
Thermodynamics of protein folding: A statistical mechanical study of a small all-beta protein
-
Guo ZY, Brooks CL. 1997. Thermodynamics of protein folding: A statistical mechanical study of a small all-beta protein. Biopolymers 42(7):745-757.
-
(1997)
Biopolymers
, vol.42
, Issue.7
, pp. 745-757
-
-
Guo, Z.Y.1
Brooks, C.L.2
-
17
-
-
36449009348
-
Folding Kinetics of Proteins - A Model Study
-
Guo ZY, Thirumalai D, Honeycutt JD. 1992. Folding Kinetics of Proteins-A Model Study. J Chem Phys 97(1):525-535.
-
(1992)
J Chem Phys
, vol.97
, Issue.1
, pp. 525-535
-
-
Guo, Z.Y.1
Thirumalai, D.2
Honeycutt, J.D.3
-
18
-
-
0033150721
-
Computer simulation of the competition between protein folding and aggregation
-
Gupta P, Hall CK, Voegler A. 1999. Computer simulation of the competition between protein folding and aggregation. Fluid Phase Equilibria 160:87-93.
-
(1999)
Fluid Phase Equilibria
, vol.160
, pp. 87-93
-
-
Gupta, P.1
Hall, C.K.2
Voegler, A.3
-
19
-
-
0031696773
-
Effect of denaturant and protein concentrations upon protein refolding and aggregation: A simple lattice model
-
Gupta P, Hall CK, Voegler AC. 1998. Effect of denaturant and protein concentrations upon protein refolding and aggregation: A simple lattice model. Protein Sci 7(12):2642-2652.
-
(1998)
Protein Sci
, vol.7
, Issue.12
, pp. 2642-2652
-
-
Gupta, P.1
Hall, C.K.2
Voegler, A.C.3
-
20
-
-
0035079856
-
Conformation propagation with prion-like characteristics in a simple model of protein folding
-
Harrison P, Chan HS, Prusiner S, Cohen F. 2001. Conformation propagation with prion-like characteristics in a simple model of protein folding. Protein Sci 10:819-835.
-
(2001)
Protein Sci
, vol.10
, pp. 819-835
-
-
Harrison, P.1
Chan, H.S.2
Prusiner, S.3
Cohen, F.4
-
21
-
-
0033582587
-
Thermodynamics of model prions and its implications for the problem of prion protein folding
-
Harrison PM, Chan HS, Prusiner SB, Cohen FE. 1999. Thermodynamics of model prions and its implications for the problem of prion protein folding. J Mol Biol 286(2):593-606.
-
(1999)
J Mol Biol
, vol.286
, Issue.2
, pp. 593-606
-
-
Harrison, P.M.1
Chan, H.S.2
Prusiner, S.B.3
Cohen, F.E.4
-
22
-
-
0026643094
-
The nature of folded states of globular proteins
-
Honeycutt JD, Thirumalai D. 1992. The nature of folded states of globular proteins. Biolpolymers 32:695-709.
-
(1992)
Biolpolymers
, vol.32
, pp. 695-709
-
-
Honeycutt, J.D.1
Thirumalai, D.2
-
23
-
-
0032994142
-
Lattice simulations of aggregation funnels for protein folding
-
Istrail S, Schwartz R, King J. 1999. Lattice simulations of aggregation funnels for protein folding. J Comput Biol 6(2): 143-162.
-
(1999)
J Comput Biol
, vol.6
, Issue.2
, pp. 143-162
-
-
Istrail, S.1
Schwartz, R.2
King, J.3
-
24
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar S, Bouzida D, Swendsen R, Kollman PA, Rosenberg JA. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comp Chem 13(8):1011-1021.
-
(1992)
J Comp Chem
, vol.13
, Issue.8
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.3
Kollman, P.A.4
Rosenberg, J.A.5
-
25
-
-
0345490880
-
Solvent-amino acid interaction energies in 3-D-lattice MC simulations of model proteins. Aggregation thermodynamics and kinetics
-
Leonhard K, Prausnitz JM, Radke CJ. 2003. Solvent-amino acid interaction energies in 3-D-lattice MC simulations of model proteins. Aggregation thermodynamics and kinetics. Phys Chem Chem Phys 5(23):5291-5299.
-
(2003)
Phys Chem Chem Phys
, vol.5
, Issue.23
, pp. 5291-5299
-
-
Leonhard, K.1
Prausnitz, J.M.2
Radke, C.J.3
-
27
-
-
0036772580
-
Preparative protein refolding
-
Middelberg AP. 2002. Preparative protein refolding. Trends Biotechnol 20(10):437-443.
-
(2002)
Trends Biotechnol
, vol.20
, Issue.10
, pp. 437-443
-
-
Middelberg, A.P.1
-
28
-
-
0032568599
-
Folding funnels and frustration in off-lattice minimalist protein landscapes
-
Nymeyer H, Garcia AE, Onuchic JN. 1998. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc Natl Acad Sci USA 95(11):5921-5928.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.11
, pp. 5921-5928
-
-
Nymeyer, H.1
Garcia, A.E.2
Onuchic, J.N.3
-
29
-
-
0034255027
-
A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro
-
Ramirez-Alvarado M, Merkel JS, Regan L. 2000. A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro. Proc Natl Acad Sci USA 97(16):8979-8984.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.16
, pp. 8979-8984
-
-
Ramirez-Alvarado, M.1
Merkel, J.S.2
Regan, L.3
-
30
-
-
0034001362
-
Proline inhibits aggregation during protein refolding
-
Samuel D, Kumar TK, Ganesh G, Jayaraman G, Yang PW, Chang MM, Trivedi VD, Wang SL, Hwang KC, Chang DK and others. 2000. Proline inhibits aggregation during protein refolding. Protein Sci 9(2):344-352.
-
(2000)
Protein Sci
, vol.9
, Issue.2
, pp. 344-352
-
-
Samuel, D.1
Kumar, T.K.2
Ganesh, G.3
Jayaraman, G.4
Yang, P.W.5
Chang, M.M.6
Trivedi, V.D.7
Wang, S.L.8
Hwang, K.C.9
Chang, D.K.10
-
31
-
-
0035055990
-
Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues
-
Schwartz R, Istrail S, King J. 2001. Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues. Protein Sci 10:1023-1031.
-
(2001)
Protein Sci
, vol.10
, pp. 1023-1031
-
-
Schwartz, R.1
Istrail, S.2
King, J.3
-
32
-
-
0000870658
-
Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist beta-barrel model
-
Shea JE, Nochomovitz YD, Guo ZY, Brooks CL. 1998. Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist beta-barrel model. J Chem Phys 109(7):2895-2903.
-
(1998)
J Chem Phys
, vol.109
, Issue.7
, pp. 2895-2903
-
-
Shea, J.E.1
Nochomovitz, Y.D.2
Guo, Z.Y.3
Brooks, C.L.4
-
33
-
-
0035823222
-
Protein refolding versus aggregation: Computer simulations on an intermediate-resolution protein model
-
Smith AV, Hall CK. 2001. Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model. J Mol Biol 312(1):187-202.
-
(2001)
J Mol Biol
, vol.312
, Issue.1
, pp. 187-202
-
-
Smith, A.V.1
Hall, C.K.2
-
34
-
-
0032726519
-
Redesigning the hydrophobic core of a model beta-sheet protein
-
Sorenson J, Head-Gordon T. 1999. Redesigning the hydrophobic core of a model beta-sheet protein. Proteins: Struct Funct Gen 37:582-591.
-
(1999)
Proteins: Struct Funct Gen
, vol.37
, pp. 582-591
-
-
Sorenson, J.1
Head-Gordon, T.2
-
35
-
-
0033693141
-
Matching simulation and experiment: A new simplified model for protein folding
-
Sorenson J, Head-Gordon T. 2000. Matching simulation and experiment: A new simplified model for protein folding. J Comp Biol 7(3/4): 469-481.
-
(2000)
J Comp Biol
, vol.7
, Issue.3-4
, pp. 469-481
-
-
Sorenson, J.1
Head-Gordon, T.2
-
36
-
-
0036207492
-
Protein engineering study of protein L by simulation
-
Sorenson J, Head-Gordon T. 2002a. Protein engineering study of protein L by simulation. J Comp Biol 9(1):35-54.
-
(2002)
J Comp Biol
, vol.9
, Issue.1
, pp. 35-54
-
-
Sorenson, J.1
Head-Gordon, T.2
-
37
-
-
0036499417
-
Toward minimalist models of larger proteins: A ubiquitin like protein
-
Sorenson J, Head-Gordon T. 2002b. Toward minimalist models of larger proteins: A ubiquitin like protein. Proteins: Struct Funct Gen 46:368-379.
-
(2002)
Proteins: Struct Funct Gen
, vol.46
, pp. 368-379
-
-
Sorenson, J.1
Head-Gordon, T.2
-
38
-
-
0141990950
-
Effect of gatekeepers on the early folding kinetics of a model beta-barrel protein
-
Stoycheva AD, Onuchic JN, Brooks CL. 2003. Effect of gatekeepers on the early folding kinetics of a model beta-barrel protein. J Chem Phys 119(11):5722-5729.
-
(2003)
J Chem Phys
, vol.119
, Issue.11
, pp. 5722-5729
-
-
Stoycheva, A.D.1
Onuchic, J.N.2
Brooks, C.L.3
-
39
-
-
0033117927
-
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
-
Thirumalai D, Klimov DK. 1999. Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol 9(2):197-207.
-
(1999)
Curr Opin Struct Biol
, vol.9
, Issue.2
, pp. 197-207
-
-
Thirumalai, D.1
Klimov, D.K.2
-
40
-
-
0001103473
-
Kinetics of folding of proteins and RNA
-
Thirumalai D, Woodson SA. 1996. Kinetics of folding of proteins and RNA. Acct Chem Res 29:433-439.
-
(1996)
Acct Chem Res
, vol.29
, pp. 433-439
-
-
Thirumalai, D.1
Woodson, S.A.2
-
41
-
-
0034208964
-
A lattice model study of macromolecular ensembles of protein models
-
Toma L, Toma S. 2000. A lattice model study of macromolecular ensembles of protein models. Biomacromolecules 1:232-238.
-
(2000)
Biomacromolecules
, vol.1
, pp. 232-238
-
-
Toma, L.1
Toma, S.2
-
42
-
-
0035815664
-
Evidence for a partially folded intermediate in alpha-synuclein fibril formation
-
Uversky VN, Li J, Fink AL. 2001. Evidence for a partially folded intermediate in alpha-synuclein fibril formation. J Biol Chem 276(14): 10737-10744.
-
(2001)
J Biol Chem
, vol.276
, Issue.14
, pp. 10737-10744
-
-
Uversky, V.N.1
Li, J.2
Fink, A.L.3
-
43
-
-
0030624384
-
Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties
-
Veitshans T, Klimov D, Thirumalai D. 1997. Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des 2(1):1-22.
-
(1997)
Fold Des
, vol.2
, Issue.1
, pp. 1-22
-
-
Veitshans, T.1
Klimov, D.2
Thirumalai, D.3
|