-
1
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(4096):223-230.
-
(1973)
Science
, vol.181
, Issue.4096
, pp. 223-230
-
-
Anfinsen, C.B.1
-
2
-
-
0023449962
-
Spin glasses and the statistical mechanics of protein folding
-
Bryngelson JD, Wolynes PG (1987) Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 84(21):7524-7528.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, Issue.21
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
3
-
-
0026723063
-
Protein folding funnels: A kinetic approach to the sequence-structure relationship
-
Leopold PE, Montal M, Onuchic JN (1992) Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc Natl Acad Sci USA 89(18):8721-8725.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, Issue.18
, pp. 8721-8725
-
-
Leopold, P.E.1
Montal, M.2
Onuchic, J.N.3
-
4
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21(3):167-195.
-
(1995)
Proteins
, vol.21
, Issue.3
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
5
-
-
12944327750
-
Energy landscapes and solved protein-folding problems
-
discussion 464-467
-
Wolynes PG (2005) Energy landscapes and solved protein-folding problems. Philos Trans A Math Phys Eng Sci 363(1827):453-464, discussion 464-467.
-
(2005)
Philos Trans a Math Phys Eng Sci
, vol.363
, Issue.1827
, pp. 453-464
-
-
Wolynes, P.G.1
-
6
-
-
33845343261
-
Membrane-protein topology
-
von Heijne G (2006) Membrane-protein topology. Nat Rev Mol Cell Biol 7(12): 909-918.
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, Issue.12
, pp. 909-918
-
-
Von Heijne, G.1
-
7
-
-
0019887931
-
Refolding of an integral membrane protein: Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments
-
Huang KS, Bayley H, Liao MJ, London E, Khorana HG (1981) Refolding of an integral membrane protein: Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments. Journal of Biological Chemistry 256(8):3802-3809.
-
(1981)
Journal of Biological Chemistry
, vol.256
, Issue.8
, pp. 3802-3809
-
-
Huang, K.S.1
Bayley, H.2
Liao, M.J.3
London, E.4
Khorana, H.G.5
-
8
-
-
84865293045
-
A successful change of circumstance: A transition state for membrane protein folding
-
Booth PJ (2012) A successful change of circumstance: A transition state for membrane protein folding. Curr Opin Struct Biol 22(4):469-475.
-
(2012)
Curr Opin Struct Biol
, vol.22
, Issue.4
, pp. 469-475
-
-
Booth, P.J.1
-
9
-
-
58849112736
-
The transition state for integral membrane protein folding
-
Curnow P, Booth PJ (2009) The transition state for integral membrane protein folding. Proc Natl Acad Sci USA 106(3):773-778.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.3
, pp. 773-778
-
-
Curnow, P.1
Booth, P.J.2
-
10
-
-
78650454699
-
Mapping the folding pathway of the transmembrane protein DsbB by protein engineering
-
Otzen DE (2011) Mapping the folding pathway of the transmembrane protein DsbB by protein engineering. Protein Eng Des Sel 24(1-2):139-149.
-
(2011)
Protein Eng des Sel
, vol.24
, Issue.1-2
, pp. 139-149
-
-
Otzen, D.E.1
-
11
-
-
84861038844
-
Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions
-
Schramm CA, et al. (2012) Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Structure 20(5):924-935.
-
(2012)
Structure
, vol.20
, Issue.5
, pp. 924-935
-
-
Schramm, C.A.1
-
12
-
-
84864213700
-
AWSEM-MD: Protein structure prediction using coarsegrained physical potentials and bioinformatically based local structure biasing
-
Davtyan A, et al. (2012) AWSEM-MD: Protein structure prediction using coarsegrained physical potentials and bioinformatically based local structure biasing. J Phys Chem B 116(29):8494-8503.
-
(2012)
J Phys Chem B
, vol.116
, Issue.29
, pp. 8494-8503
-
-
Davtyan, A.1
-
13
-
-
0026716643
-
Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
-
von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225(2):487-494.
-
(1992)
J Mol Biol
, vol.225
, Issue.2
, pp. 487-494
-
-
Von Heijne, G.1
-
14
-
-
0042868638
-
Role of water mediated interactions in protein-protein recognition landscapes
-
DOI 10.1021/ja034729u
-
Papoian GA, Ulander J, Wolynes PG (2003) Role of water mediated interactions in protein-protein recognition landscapes. J Am Chem Soc 125(30):9170-9178. (Pubitemid 36903833)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.30
, pp. 9170-9178
-
-
Papoian, G.A.1
Ulander, J.2
Wolynes, P.G.3
-
15
-
-
1542618345
-
Water in protein structure prediction
-
DOI 10.1073/pnas.0307851100
-
Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG (2004) Water in protein structure prediction. Proc Natl Acad Sci USA 101(10):3352-3357. (Pubitemid 38338198)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.10
, pp. 3352-3357
-
-
Papoian, G.A.1
Ulander, J.2
Eastwood, M.P.3
Luthey-Schulten, Z.4
Wolynes, P.G.5
-
17
-
-
13444280419
-
PDB-TM: Selection and membrane localization of transmembrane proteins in the protein data bank
-
DOI 10.1093/nar/gki002
-
Tusnády GE, Dosztányi Z, Simon I (2005) PDB-TM: Selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 33(Database issue):D275-D278. (Pubitemid 40207877)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Tusnady, G.E.1
Dosztanyi, Z.2
Simon, I.3
-
18
-
-
67649472570
-
Transmembrane protein topology prediction using support vector machines
-
Nugent T, Jones DT (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics 10:159.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 159
-
-
Nugent, T.1
Jones, D.T.2
-
19
-
-
0347417009
-
Optimizing Physical Energy Functions for Protein Folding
-
DOI 10.1002/prot.10429
-
Fujitsuka Y, Takada S, Luthey-Schulten ZA, Wolynes PG (2004) Optimizing physical energy functions for protein folding. Proteins 54(1):88-103. (Pubitemid 38036917)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.54
, Issue.1
, pp. 88-103
-
-
Fujitsuka, Y.1
Takada, S.2
Luthey-Schulten, Z.A.3
Wolynes, P.G.4
-
20
-
-
84869784991
-
Predictive energy landscapes for protein-protein association
-
Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG (2012) Predictive energy landscapes for protein-protein association. Proc Natl Acad Sci USA 109(47):19244-19249.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.47
, pp. 19244-19249
-
-
Zheng, W.1
Schafer, N.P.2
Davtyan, A.3
Papoian, G.A.4
Wolynes, P.G.5
-
21
-
-
84885460398
-
Funneling and frustration in the energy landscapes of some designed and simplified proteins
-
Truong HH, Kim BL, Schafer NP, Wolynes PG (2013) Funneling and frustration in the energy landscapes of some designed and simplified proteins. J Chem Phys 139(12):121908.
-
(2013)
J Chem Phys
, vol.139
, Issue.12
, pp. 121908
-
-
Truong, H.H.1
Kim, B.L.2
Schafer, N.P.3
Wolynes, P.G.4
-
22
-
-
84873105668
-
Frustration in the energy landscapes of multidomain protein misfolding
-
Zheng W, Schafer NP, Wolynes PG (2013) Frustration in the energy landscapes of multidomain protein misfolding. Proc Natl Acad Sci USA 110(5):1680-1685.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.5
, pp. 1680-1685
-
-
Zheng, W.1
Schafer, N.P.2
Wolynes, P.G.3
-
23
-
-
84890847498
-
Free energy landscapes for initiation and branching of protein aggregation
-
Zheng W, Schafer NP, Wolynes PG (2013) Free energy landscapes for initiation and branching of protein aggregation. Proc Natl Acad Sci USA 110(51):20515-20520.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.51
, pp. 20515-20520
-
-
Zheng, W.1
Schafer, N.P.2
Wolynes, P.G.3
-
24
-
-
0025148817
-
A simple statistical field theory of heteropolymer collapse with application to protein folding
-
DOI 10.1002/bip.360300117
-
Bryngelson JD, Wolynes PG (1990) A simple statistical field theory of heteropolymer collapse with application to protein folding. Biopolymers 30(1-2):177-188. (Pubitemid 20263101)
-
(1990)
Biopolymers
, vol.30
, Issue.1-2
, pp. 177-188
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
25
-
-
0346882663
-
ModLoop: Automated modeling of loops in protein structures
-
DOI 10.1093/bioinformatics/btg362
-
Fiser A, Sali A (2003) ModLoop: Automated modeling of loops in protein structures. Bioinformatics 19(18):2500-2501. (Pubitemid 38016660)
-
(2003)
Bioinformatics
, vol.19
, Issue.18
, pp. 2500-2501
-
-
Fiser, A.1
Sali, A.2
-
26
-
-
0033983453
-
Asparagine-mediated selfassociation of a model transmembrane helix
-
Choma C, Gratkowski H, Lear JD, DeGrado WF (2000) Asparagine-mediated selfassociation of a model transmembrane helix. Nat Struct Biol 7(2):161 - 166.
-
(2000)
Nat Struct Biol
, vol.7
, Issue.2
, pp. 161-166
-
-
Choma, C.1
Gratkowski, H.2
Lear, J.D.3
DeGrado, W.F.4
-
27
-
-
0035969998
-
Polar side chains drive the association of model transmembrane peptides
-
Gratkowski H, Lear JD, DeGrado WF (2001) Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci USA 98(3):880- 885.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.3
, pp. 880-885
-
-
Gratkowski, H.1
Lear, J.D.2
DeGrado, W.F.3
-
29
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
DOI 10.1002/prot.340230412
-
Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23(4):566-579. (Pubitemid 26009520)
-
(1995)
Proteins: Structure, Function and Genetics
, vol.23
, Issue.4
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
30
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11(9):739-747. (Pubitemid 28434482)
-
(1998)
Protein Engineering
, vol.11
, Issue.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
31
-
-
52949088587
-
Statistically optimal analysis of samples from multiple equilibrium states
-
Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 129(12):124105.
-
(2008)
J Chem Phys
, vol.129
, Issue.12
, pp. 124105
-
-
Shirts, M.R.1
Chodera, J.D.2
-
32
-
-
14044275168
-
Symmetry and frustration in protein energy landscapes: A near degeneracy resolves the ROD dimer-folding mystery
-
DOI 10.1073/pnas.0409572102
-
Levy Y, Cho SS, Shen T, Onuchic JN, Wolynes PG (2005) Symmetry and frustration in protein energy landscapes: A near degeneracy resolves the Rop dimer-folding mystery. Proc Natl Acad Sci USA 102(7):2373-2378. (Pubitemid 40279383)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.7
, pp. 2373-2378
-
-
Levy, Y.1
Cho, S.S.2
Shen, T.3
Onuchic, J.N.4
Wolynes, P.G.5
-
33
-
-
84862301192
-
Mirror images as naturally competing conformations in protein folding
-
Noel JK, et al. (2012) Mirror images as naturally competing conformations in protein folding. J Phys Chem B 116(23):6880-6888.
-
(2012)
J Phys Chem B
, vol.116
, Issue.23
, pp. 6880-6888
-
-
Noel, J.K.1
|