-
1
-
-
0024533979
-
Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig alpha-lactalbumin
-
Baum J, Dobson CM, Evans PA, Hanley C, (1989) Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig alpha-lactalbumin. Biochemistry 28: 7-13.
-
(1989)
Biochemistry
, vol.28
, pp. 7-13
-
-
Baum, J.1
Dobson, C.M.2
Evans, P.A.3
Hanley, C.4
-
2
-
-
0027433511
-
Intermediate conformational states of apocytochrome c
-
Hamada D, Hoshino M, Kataoka M, Fink AL, Goto Y, (1993) Intermediate conformational states of apocytochrome c. Biochemistry 32: 10351-10358.
-
(1993)
Biochemistry
, vol.32
, pp. 10351-10358
-
-
Hamada, D.1
Hoshino, M.2
Kataoka, M.3
Fink, A.L.4
Goto, Y.5
-
3
-
-
0028176911
-
"Partly folded" state, a new equilibrium state of protein molecules: four-state guanidinium chloride-induced unfolding of beta-lactamase at low temperature
-
Uversky VN, Ptitsyn OB, (1994) "Partly folded" state, a new equilibrium state of protein molecules: four-state guanidinium chloride-induced unfolding of beta-lactamase at low temperature. Biochemistry 33: 2782-2791.
-
(1994)
Biochemistry
, vol.33
, pp. 2782-2791
-
-
Uversky, V.N.1
Ptitsyn, O.B.2
-
4
-
-
0035100432
-
An engineered leucine zipper a position mutant with an unusual three-state unfolding pathway
-
Zhu H, Celinski SA, Scholtz JM, Hu JC, (2001) An engineered leucine zipper a position mutant with an unusual three-state unfolding pathway. Protein Sci 10: 24-33.
-
(2001)
Protein Sci
, vol.10
, pp. 24-33
-
-
Zhu, H.1
Celinski, S.A.2
Scholtz, J.M.3
Hu, J.C.4
-
5
-
-
0037031314
-
Four-state equilibrium unfolding of an scFv antibody fragment
-
Pedroso I, Irun MP, Machicado C, Sancho J, (2002) Four-state equilibrium unfolding of an scFv antibody fragment. Biochemistry 41: 9873-9884.
-
(2002)
Biochemistry
, vol.41
, pp. 9873-9884
-
-
Pedroso, I.1
Irun, M.P.2
Machicado, C.3
Sancho, J.4
-
6
-
-
0037137182
-
From two-state to three-state: the effect of the P61A mutation on the dynamics and stability of the factor for inversion stimulation results in an altered equilibrium denaturation mechanism
-
Hobart SA, Meinhold DW, Osuna R, Colon W, (2002) From two-state to three-state: the effect of the P61A mutation on the dynamics and stability of the factor for inversion stimulation results in an altered equilibrium denaturation mechanism. Biochemistry 41: 13744-13754.
-
(2002)
Biochemistry
, vol.41
, pp. 13744-13754
-
-
Hobart, S.A.1
Meinhold, D.W.2
Osuna, R.3
Colon, W.4
-
7
-
-
0038047141
-
Dynamics of the core tryptophan during the formation of a productive molten globule intermediate of barstar
-
Rami BR, Krishnamoorthy G, Udgaonkar JB, (2003) Dynamics of the core tryptophan during the formation of a productive molten globule intermediate of barstar. Biochemistry 42: 7986-8000.
-
(2003)
Biochemistry
, vol.42
, pp. 7986-8000
-
-
Rami, B.R.1
Krishnamoorthy, G.2
Udgaonkar, J.B.3
-
8
-
-
0037434840
-
The active site of pepsin is formed in the intermediate conformation dominant at mildly acidic pH
-
Campos LA, Sancho J, (2003) The active site of pepsin is formed in the intermediate conformation dominant at mildly acidic pH. FEBS Lett 538: 89-95.
-
(2003)
FEBS Lett
, vol.538
, pp. 89-95
-
-
Campos, L.A.1
Sancho, J.2
-
9
-
-
0346118882
-
Folding intermediates of the prion protein stabilized by hydrostatic pressure and low temperature
-
Martins SM, Chapeaurouge A, Ferreira ST, (2003) Folding intermediates of the prion protein stabilized by hydrostatic pressure and low temperature. J Biol Chem 278: 50449-50455.
-
(2003)
J Biol Chem
, vol.278
, pp. 50449-50455
-
-
Martins, S.M.1
Chapeaurouge, A.2
Ferreira, S.T.3
-
10
-
-
0031815749
-
How do small single-domain proteins fold?
-
Jackson SE, (1998) How do small single-domain proteins fold? Folding Des 3: R81-R91.
-
(1998)
Folding Des
, vol.3
-
-
Jackson, S.E.1
-
11
-
-
0030010408
-
Intermediate states in protein folding
-
Privalov PL, (1996) Intermediate states in protein folding. J Mol Biol 258: 707-725.
-
(1996)
J Mol Biol
, vol.258
, pp. 707-725
-
-
Privalov, P.L.1
-
12
-
-
0023644891
-
Conformations of intermediates in the folding of the pancreatic trypsin inhibitor
-
States DJ, Creighton TE, Dobson CM, Karplus M, (1987) Conformations of intermediates in the folding of the pancreatic trypsin inhibitor. J Mol Biol 195: 731-739.
-
(1987)
J Mol Biol
, vol.195
, pp. 731-739
-
-
States, D.J.1
Creighton, T.E.2
Dobson, C.M.3
Karplus, M.4
-
13
-
-
0028856292
-
Defective protein folding as a basis of human disease
-
Thomas PJ, Qu BH, Pedersen PL, (1995) Defective protein folding as a basis of human disease. Trends Biochem Sci 20: 456-459.
-
(1995)
Trends Biochem Sci
, vol.20
, pp. 456-459
-
-
Thomas, P.J.1
Qu, B.H.2
Pedersen, P.L.3
-
16
-
-
0029001772
-
Disruption of the gene for hsp30, an alpha-crystallin-related heat shock protein of Neurospora crassa, causes defects in thermotolerance
-
Plesofsky-Vig N, Brambl R, (1995) Disruption of the gene for hsp30, an alpha-crystallin-related heat shock protein of Neurospora crassa, causes defects in thermotolerance. Proc Natl Acad Sci U S A 92: 5032-5036.
-
(1995)
Proc Natl Acad Sci U S A
, vol.92
, pp. 5032-5036
-
-
Plesofsky-Vig, N.1
Brambl, R.2
-
17
-
-
0027996115
-
Protein disaggregation mediated by heatshock protein Hsp104
-
Parsell DA, Kowal AS, Singer MA, Lindquist S, (2002) Protein disaggregation mediated by heatshock protein Hsp104. Nature 372: 475-478.
-
(2002)
Nature
, vol.372
, pp. 475-478
-
-
Parsell, D.A.1
Kowal, A.S.2
Singer, M.A.3
Lindquist, S.4
-
18
-
-
0025932041
-
A "molten-globule" membrane insertion intermediate of the pore-forming domain of colicin A
-
van der Goot FG, Gonzalez-Manas JM, Lakey JH, Pattus F, (1991) A "molten-globule" membrane insertion intermediate of the pore-forming domain of colicin A. Nature 354: 408-410.
-
(1991)
Nature
, vol.354
, pp. 408-410
-
-
van der Goot, F.G.1
Gonzalez-Manas, J.M.2
Lakey, J.H.3
Pattus, F.4
-
19
-
-
0026785238
-
Retinol-binding protein is in the molten globule state at low pH
-
Bychkova VE, Berni R, Rossi GL, Kutyshenko P, Ptitsyn OB, (1992) Retinol-binding protein is in the molten globule state at low pH. Biochemistry 31: 7566-7571.
-
(1992)
Biochemistry
, vol.31
, pp. 7566-7571
-
-
Bychkova, V.E.1
Berni, R.2
Rossi, G.L.3
Kutyshenko, P.4
Ptitsyn, O.B.5
-
20
-
-
0030806303
-
Ligand-free form of human-fetoprotein: evidence for the molten globule state
-
Uversky VN, Narizhneva NV, Ivanova TV, Kirkitadze MD, Tomashevski AY, (1997) Ligand-free form of human-fetoprotein: evidence for the molten globule state. FEBS Lett 410: 280-284.
-
(1997)
FEBS Lett
, vol.410
, pp. 280-284
-
-
Uversky, V.N.1
Narizhneva, N.V.2
Ivanova, T.V.3
Kirkitadze, M.D.4
Tomashevski, A.Y.5
-
21
-
-
0035909839
-
Role of the disulfide cleavage induced molten globule state of type A botulinum neurotoxin in its endopeptidase activity
-
Cai S, Singh BR, (2001) Role of the disulfide cleavage induced molten globule state of type A botulinum neurotoxin in its endopeptidase activity. Biochemistry 40: 15327-15333.
-
(2001)
Biochemistry
, vol.40
, pp. 15327-15333
-
-
Cai, S.1
Singh, B.R.2
-
23
-
-
0027536094
-
Structure and dynamics of the acid-denatured molten globule state of alpha-lactalbumin: a two-dimensional NMR study
-
Alexandrescu AT, Evans PA, Pitkeathly M, Baum J, Dobson CM, (1993) Structure and dynamics of the acid-denatured molten globule state of alpha-lactalbumin: a two-dimensional NMR study. Biochemistry 32: 1707-1718.
-
(1993)
Biochemistry
, vol.32
, pp. 1707-1718
-
-
Alexandrescu, A.T.1
Evans, P.A.2
Pitkeathly, M.3
Baum, J.4
Dobson, C.M.5
-
24
-
-
0030768045
-
A residue-specific NMR view of the noncooperative unfolding of a molten globule
-
Schulman BA, Kim PS, Dobson CM, Redfield C, (1997) A residue-specific NMR view of the noncooperative unfolding of a molten globule. Nat Struct Biol 4: 630-634.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 630-634
-
-
Schulman, B.A.1
Kim, P.S.2
Dobson, C.M.3
Redfield, C.4
-
25
-
-
0031064317
-
Triple-resonance NOESY-based experiments with improved spectral resolution: applications to structural characterization of unfolded, partially folded and folded proteins
-
Zhang O, Forman-Kay JD, Shortle D, Kay LE, (1997) Triple-resonance NOESY-based experiments with improved spectral resolution: applications to structural characterization of unfolded, partially folded and folded proteins. J Biomol NMR 9: 181-200.
-
(1997)
J Biomol NMR
, vol.9
, pp. 181-200
-
-
Zhang, O.1
Forman-Kay, J.D.2
Shortle, D.3
Kay, L.E.4
-
26
-
-
0032539590
-
Molten globule unfolding monitored by hydrogen exchange in urea
-
Chamberlain AK, Marqusee S, (1998) Molten globule unfolding monitored by hydrogen exchange in urea. Biochemistry 37: 1736-1742.
-
(1998)
Biochemistry
, vol.37
, pp. 1736-1742
-
-
Chamberlain, A.K.1
Marqusee, S.2
-
27
-
-
0031932824
-
Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding
-
Eliezer D, Yao J, Dyson JH, Wright PE, (1998) Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding. Nat Struct Biol 5: 148-155.
-
(1998)
Nat Struct Biol
, vol.5
, pp. 148-155
-
-
Eliezer, D.1
Yao, J.2
Dyson, J.H.3
Wright, P.E.4
-
28
-
-
0037675760
-
Structural characterisation of the human a-lactalbumin molten globule at high temperature
-
Ramboarina S, Redfield C, (2003) Structural characterisation of the human a-lactalbumin molten globule at high temperature. J Mol Biol 330: 1177-1188.
-
(2003)
J Mol Biol
, vol.330
, pp. 1177-1188
-
-
Ramboarina, S.1
Redfield, C.2
-
29
-
-
0026511656
-
The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
-
Fersht AR, Matouschek A, Serrano L, (1992) The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol 224: 771-782.
-
(1992)
J Mol Biol
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
30
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek A, Kellis JT Jr, Serrano L, Fersht AR, (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340: 122-126.
-
(1989)
Nature
, vol.340
, pp. 122-126
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Fersht, A.R.4
-
31
-
-
0025698613
-
Transient folding intermediates characterized by protein engineering
-
Matouschek A, Kellis JT Jr, Serrano L, Bycroft M, Fersht AR, (1990) Transient folding intermediates characterized by protein engineering. Nature 346: 440-445.
-
(1990)
Nature
, vol.346
, pp. 440-445
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Bycroft, M.4
Fersht, A.R.5
-
32
-
-
0026694167
-
A model of the molten globule state from molecular dynamics simulations
-
Daggett V, Levitt M, (1992) A model of the molten globule state from molecular dynamics simulations. Proc Natl Acad Sci U S A 89: 5142-5146.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 5142-5146
-
-
Daggett, V.1
Levitt, M.2
-
33
-
-
0026630480
-
Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state
-
Mark AE, van Gunsteren WF, (1992) Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state. Biochemistry 31: 7745-7748.
-
(1992)
Biochemistry
, vol.31
, pp. 7745-7748
-
-
Mark, A.E.1
van Gunsteren, W.F.2
-
34
-
-
0027219504
-
Protein unfolding pathways explored through molecular dynamics simulations
-
Daggett V, Levitt M, (1993) Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol 232: 600-619.
-
(1993)
J Mol Biol
, vol.232
, pp. 600-619
-
-
Daggett, V.1
Levitt, M.2
-
35
-
-
0027316216
-
Molecular dynamics simulations of the unfolding of apomyoglobin in water
-
Tirado-Rives J, Jorgensen WL, (1993) Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry 32: 4175-4184.
-
(1993)
Biochemistry
, vol.32
, pp. 4175-4184
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
36
-
-
0028264860
-
Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase
-
Caflisch A, Karplus M, (1994) Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci U S A 91: 1746-1750.
-
(1994)
Proc Natl Acad Sci U S A
, vol.91
, pp. 1746-1750
-
-
Caflisch, A.1
Karplus, M.2
-
37
-
-
0028965968
-
Molecular dynamics simulations of protein unfolding and limited refolding: Characterization of partially unfolded states of ubiquitin in 60% methanol and in water
-
Alonso D, Daggett V, (1995) Molecular dynamics simulations of protein unfolding and limited refolding: Characterization of partially unfolded states of ubiquitin in 60% methanol and in water. J Mol Biol 247: 501-520.
-
(1995)
J Mol Biol
, vol.247
, pp. 501-520
-
-
Alonso, D.1
Daggett, V.2
-
38
-
-
0031465967
-
"New view" of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T, Karplus M, (1997) "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278: 1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
39
-
-
0030939289
-
Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea
-
Tirado-Rives J, Orozco M, Jorgensen WL, (1997) Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry 36: 7313-7329.
-
(1997)
Biochemistry
, vol.36
, pp. 7313-7329
-
-
Tirado-Rives, J.1
Orozco, M.2
Jorgensen, W.L.3
-
40
-
-
0345411345
-
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
-
Tsai J, Levitt M, Baker D, (1999) Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol 291: 215-225.
-
(1999)
J Mol Biol
, vol.291
, pp. 215-225
-
-
Tsai, J.1
Levitt, M.2
Baker, D.3
-
41
-
-
0033548540
-
Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin
-
Smith LJ, Dobson CM, van Gunsteren WF, (1999) Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin. J Mol Biol 286: 1567-1580.
-
(1999)
J Mol Biol
, vol.286
, pp. 1567-1580
-
-
Smith, L.J.1
Dobson, C.M.2
van Gunsteren, W.F.3
-
42
-
-
0034610360
-
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
-
Mayor U, Johnson CM, Daggett V, Fersht AR, (2000) Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci U S A 97: 13518-13522.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 13518-13522
-
-
Mayor, U.1
Johnson, C.M.2
Daggett, V.3
Fersht, A.R.4
-
43
-
-
0035793221
-
Characterization of NMR relaxation-active motions of a partially folded A-state analogue of ubiquitin
-
Prompers JJ, Scheurer C, Brüschweiler R, (2001) Characterization of NMR relaxation-active motions of a partially folded A-state analogue of ubiquitin. J Mol Biol 305: 1085-1097.
-
(2001)
J Mol Biol
, vol.305
, pp. 1085-1097
-
-
Prompers, J.J.1
Scheurer, C.2
Brüschweiler, R.3
-
44
-
-
0036280655
-
Molecular dynamics simulations of the protein unfolding/folding reaction
-
Daggett V, (2002) Molecular dynamics simulations of the protein unfolding/folding reaction. Acc Chem Res 35: 422-429.
-
(2002)
Acc Chem Res
, vol.35
, pp. 422-429
-
-
Daggett, V.1
-
45
-
-
33646052947
-
Flavodoxins: sequence, folding, binding, function and beyond
-
Sancho J, (2006) Flavodoxins: sequence, folding, binding, function and beyond. Cell Mol Life Sci 63: 855-864.
-
(2006)
Cell Mol Life Sci
, vol.63
, pp. 855-864
-
-
Sancho, J.1
-
46
-
-
0029943149
-
Conformational stability of apoflavodoxin
-
Genzor CG, Beldarrain A, Gomez-Moreno C, Lopez-Lacomba JL, Cortijo M, et al. (1996) Conformational stability of apoflavodoxin. Protein Sci 5: 1376-1388.
-
(1996)
Protein Sci
, vol.5
, pp. 1376-1388
-
-
Genzor, C.G.1
Beldarrain, A.2
Gomez-Moreno, C.3
Lopez-Lacomba, J.L.4
Cortijo, M.5
-
47
-
-
0035793715
-
Native hydrogen bonds in a molten globule: the apoflavodoxin thermal intermediate
-
Irun MP, Garcia-Mira MM, Sanchez-Ruiz JM, Sancho J, (2001) Native hydrogen bonds in a molten globule: the apoflavodoxin thermal intermediate. J Mol Biol 306: 877-888.
-
(2001)
J Mol Biol
, vol.306
, pp. 877-888
-
-
Irun, M.P.1
Garcia-Mira, M.M.2
Sanchez-Ruiz, J.M.3
Sancho, J.4
-
48
-
-
0034660451
-
No cofactor effect on equilibrium unfolding of Desulfovibrio desulfuricans flavodoxin
-
Apiyo D, Guidry J, Wittung-Stafshede P, (2000) No cofactor effect on equilibrium unfolding of Desulfovibrio desulfuricans flavodoxin. Biochim Biophys Acta 1479: 214-224.
-
(2000)
Biochim Biophys Acta
, vol.1479
, pp. 214-224
-
-
Apiyo, D.1
Guidry, J.2
Wittung-Stafshede, P.3
-
49
-
-
13444280296
-
FMN binding and unfolding of Desulfovibrio desulfuricans flavodoxin: 'hidden' intermediates at low denaturant concentrations
-
Muralidhara BK, Wittung-Stafshede P, (2005) FMN binding and unfolding of Desulfovibrio desulfuricans flavodoxin: 'hidden' intermediates at low denaturant concentrations. Biochim Biophys Acta 1747: 239-250.
-
(2005)
Biochim Biophys Acta
, vol.1747
, pp. 239-250
-
-
Muralidhara, B.K.1
Wittung-Stafshede, P.2
-
50
-
-
0036156208
-
A comparison of the urea-induced unfolding of apoflavodoxin and flavodoxin from Desulfovibrio vulgaris
-
Nuallain BO, Mayhew SG, (2002) A comparison of the urea-induced unfolding of apoflavodoxin and flavodoxin from Desulfovibrio vulgaris. Eur J Biochem 269: 212-223.
-
(2002)
Eur J Biochem
, vol.269
, pp. 212-223
-
-
Nuallain, B.O.1
Mayhew, S.G.2
-
51
-
-
0029989460
-
Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apo flavodoxin
-
Genzor CG, Perales-Alcon A, Sancho J, Romero A, (1996) Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apo flavodoxin. Nat Struct Biol 3: 329-332.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 329-332
-
-
Genzor, C.G.1
Perales-Alcon, A.2
Sancho, J.3
Romero, A.4
-
52
-
-
0035371555
-
Anabaena apoflavodoxin hydrogen exchange: on the stable exchange core of the alpha/beta(21345) flavodoxinlike family
-
Langdon GM, Jimenez MA, Genzor CG, Maldonado S, Sancho J, et al. (2001) Anabaena apoflavodoxin hydrogen exchange: on the stable exchange core of the alpha/beta(21345) flavodoxinlike family. Proteins 43: 476-488.
-
(2001)
Proteins
, vol.43
, pp. 476-488
-
-
Langdon, G.M.1
Jimenez, M.A.2
Genzor, C.G.3
Maldonado, S.4
Sancho, J.5
-
53
-
-
7044231161
-
Structure of stable protein folding intermediates by equilibrium phi-analysis: the apoflavodoxin thermal intermediate
-
Campos LA, Bueno M, Lopez-Llano J, Jimenez MA, Sancho J, (2004) Structure of stable protein folding intermediates by equilibrium phi-analysis: the apoflavodoxin thermal intermediate. J Mol Biol 344: 239-255.
-
(2004)
J Mol Biol
, vol.344
, pp. 239-255
-
-
Campos, L.A.1
Bueno, M.2
Lopez-Llano, J.3
Jimenez, M.A.4
Sancho, J.5
-
54
-
-
79951675082
-
Structural analysis of an equilibrium holding intermediate in the apoflavodoxin native ensemble by Small-angle X-ray scattering
-
Ayuso-Tejedor S, García-Fandiño R, Orozco M, Sancho J, Bernadó P, (2011) Structural analysis of an equilibrium holding intermediate in the apoflavodoxin native ensemble by Small-angle X-ray scattering. J Mol Biol 406: 604-619.
-
(2011)
J Mol Biol
, vol.406
, pp. 604-619
-
-
Ayuso-Tejedor, S.1
García-Fandiño, R.2
Orozco, M.3
Sancho, J.4
Bernadó, P.5
-
55
-
-
0035576327
-
Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins
-
Gelpi JL, Kalko SG, Barril X, Cirera J, de la Cruz X, et al. (2001) Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins. Proteins 45: 428-437.
-
(2001)
Proteins
, vol.45
, pp. 428-437
-
-
Gelpi, J.L.1
Kalko, S.G.2
Barril, X.3
Cirera, J.4
de la Cruz, X.5
-
56
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey R, Klein ML, (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 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.4
Klein, M.L.5
-
57
-
-
0030873459
-
Molecular dynamics simulations of the d (T•A•T) triple helix
-
Shields G, Laughton CA, Orozco M, (1997) Molecular dynamics simulations of the d (T•A•T) triple helix. J Am Chem Soc 119: 7463-7469.
-
(1997)
J Am Chem Soc
, vol.119
, pp. 7463-7469
-
-
Shields, G.1
Laughton, C.A.2
Orozco, M.3
-
58
-
-
33846823909
-
Particle mesh Ewald - an N.Log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L, (1993) Particle mesh Ewald- an N.Log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
59
-
-
36449009053
-
Molecular dynamics algorithm for multiple time scales: Systems with disparate masses
-
Tuckerman ME, Berne BJ, (1991) Molecular dynamics algorithm for multiple time scales: Systems with disparate masses. J Chem Phys 94: 1465-1469.
-
(1991)
J Chem Phys
, vol.94
, pp. 1465-1469
-
-
Tuckerman, M.E.1
Berne, B.J.2
-
60
-
-
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 Comput Phys 52: 24-34.
-
(1983)
J Comput Phys
, vol.52
, pp. 24-34
-
-
Andersen, H.C.1
-
61
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, et al. (1999) NAMD2: Greater scalability for parallel molecular dynamics. J Comput Phys 151: 283-312.
-
(1999)
J Comput Phys
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
-
62
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
-
63
-
-
0348244547
-
All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data
-
Foloppe N, MacKerell AD Jr, (2000) All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data. J Comp Chem 21: 86-104.
-
(2000)
J Comp Chem
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell Jr., A.D.2
-
64
-
-
0041784950
-
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, et al. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J Phys Chem B 102: 3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
-
65
-
-
34247186195
-
-
University of California, San Francisco
-
Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, et al. (2006) AMBER 9, University of California, San Francisco.
-
(2006)
AMBER 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
-
66
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham III TE, et al. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Commun 91: 1-41.
-
(1995)
Comp Phys Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham III, T.E.5
-
67
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case DA, Cheatham T, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.2
Darden, T.3
Gohlke, H.4
Luo, R.5
-
68
-
-
1942423619
-
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
-
Feig M, Karanicolas J, Brooks CL 3rd, (2004) MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 22: 377-395.
-
(2004)
J Mol Graph Model
, vol.22
, pp. 377-395
-
-
Feig, M.1
Karanicolas, J.2
Brooks 3rd, C.L.3
-
69
-
-
0030339738
-
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
-
Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM, (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477-486.
-
(1996)
J Biomol NMR
, vol.8
, pp. 477-486
-
-
Laskowski, R.A.1
Rullmannn, J.A.2
MacArthur, M.W.3
Kaptein, R.4
Thornton, J.M.5
-
70
-
-
0003742069
-
-
Department of Biochemistry and Molecular Biology, University College London
-
Hubbard SJ, Thornton JM (1993) 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.
-
(1993)
'NACCESS', Computer Program
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
72
-
-
0034500645
-
Similarities between principal components of protein dynamics and random diffusion
-
Hess B, (2000) Similarities between principal components of protein dynamics and random diffusion. Phys Rev E Stat Nonlin Soft Matter Phys 62: 8438-8448.
-
(2000)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.62
, pp. 8438-8448
-
-
Hess, B.1
-
73
-
-
33645393530
-
Exploring the essential dynamics of B-DNA
-
Pérez A, Blas JR, Rueda M, López-Bes JM, de la Cruz X, et al. (2005) Exploring the essential dynamics of B-DNA. J Chem Theory Comput 1: 790-800.
-
(2005)
J Chem Theory Comput
, vol.1
, pp. 790-800
-
-
Pérez, A.1
Blas, J.R.2
Rueda, M.3
López-Bes, J.M.4
de la Cruz, X.5
-
74
-
-
34248159870
-
Thorough Validation of Protein Normal Mode Analysis- A Comparative Study with Essential Dynamics
-
Rueda M, Chacón P, Orozco M, (2007) Thorough Validation of Protein Normal Mode Analysis- A Comparative Study with Essential Dynamics. Structure 15: 565-575.
-
(2007)
Structure
, vol.15
, pp. 565-575
-
-
Rueda, M.1
Chacón, P.2
Orozco, M.3
-
75
-
-
33746534826
-
Energetics of aliphatic deletions in protein cores
-
Bueno M, Campos LA, Estrada J, Sancho J, (2006) Energetics of aliphatic deletions in protein cores. Protein Sci 15: 1858-1872.
-
(2006)
Protein Sci
, vol.15
, pp. 1858-1872
-
-
Bueno, M.1
Campos, L.A.2
Estrada, J.3
Sancho, J.4
-
76
-
-
0033531973
-
Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations
-
Paci E, Karplus M, (1999) Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J Mol Biol 288: 441-459.
-
(1999)
J Mol Biol
, vol.288
, pp. 441-459
-
-
Paci, E.1
Karplus, M.2
-
77
-
-
0141484613
-
PRIMUS: a Windows PC-based system for small-angle scattering data analysis
-
Konarev PV, Volkov VV, Sokolova AV, Koch MHJ, Svergun DI, (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr 36: 1277-1282.
-
(2003)
J Appl Crystallogr
, vol.36
, pp. 1277-1282
-
-
Konarev, P.V.1
Volkov, V.V.2
Sokolova, A.V.3
Koch, M.H.J.4
Svergun, D.I.5
-
78
-
-
0001498978
-
La Diffraction des Rayons X aux Très Faibles Angles: Applications à l'Etude des Phénomènes Ultra-microscopiques
-
Guinier A, (1939) La Diffraction des Rayons X aux Très Faibles Angles: Applications à l'Etude des Phénomènes Ultra-microscopiques. Annales de physique (Paris) 12: 161-237.
-
(1939)
Annales De Physique (Paris)
, vol.12
, pp. 161-237
-
-
Guinier, A.1
-
79
-
-
84984342002
-
Selectivity, Local Rank, 3-Way Data-Analysis and Ambiguity in Multivariate Curve Resolution
-
Tauler R, Smilde A, Kowalski B, (1995) Selectivity, Local Rank, 3-Way Data-Analysis and Ambiguity in Multivariate Curve Resolution. J Chemom 9: 31-58.
-
(1995)
J Chemom
, vol.9
, pp. 31-58
-
-
Tauler, R.1
Smilde, A.2
Kowalski, B.3
-
80
-
-
0028807247
-
Multivariate curve resolution applied to second order data
-
Tauler R, (1995) Multivariate curve resolution applied to second order data. Chemom Intell Lab Syst 30: 133-146.
-
(1995)
Chemom Intell Lab Syst
, vol.30
, pp. 133-146
-
-
Tauler, R.1
-
81
-
-
33845438591
-
Multivariate curve resolution (MCR) from 2000: Progress in concepts and applications
-
de Juan A, Tauler R, (2006) Multivariate curve resolution (MCR) from 2000: Progress in concepts and applications. Crit Rev Anal Chem 36: 163-176.
-
(2006)
Crit Rev Anal Chem
, vol.36
, pp. 163-176
-
-
de Juan, A.1
Tauler, R.2
-
82
-
-
67849117365
-
Low-Resolution Structures of Transient Protein-Protein Complexes Using Small-Angle X-ray Scattering
-
Blobel J, Bernado P, Svergun DI, Tauler R, Pons M, (2009) Low-Resolution Structures of Transient Protein-Protein Complexes Using Small-Angle X-ray Scattering. J Am Chem Soc 131: 4378-4386.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 4378-4386
-
-
Blobel, J.1
Bernado, P.2
Svergun, D.I.3
Tauler, R.4
Pons, M.5
-
83
-
-
0029185933
-
CRYSOL - A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates
-
Svergun D, Barberato C, Koch MHJ, (1995) CRYSOL- A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28: 768-773.
-
(1995)
J Appl Crystallogr
, vol.28
, pp. 768-773
-
-
Svergun, D.1
Barberato, C.2
Koch, M.H.J.3
-
84
-
-
38849142536
-
The flavodoxin from Helicobacter pylori: Structural determinants of thermostability and FMN cofactor binding
-
Cremades N, Velázquez-Campoy A, Freire E, Sancho J, (2008) The flavodoxin from Helicobacter pylori: Structural determinants of thermostability and FMN cofactor binding. Biochemistry 47: 627-639.
-
(2008)
Biochemistry
, vol.47
, pp. 627-639
-
-
Cremades, N.1
Velázquez-Campoy, A.2
Freire, E.3
Sancho, J.4
-
85
-
-
33846512402
-
A consensous view to Protein Dynamics
-
Rueda M, Ferrer C, Meyer T, Pérez A, Camps J, et al. (2007) A consensous view to Protein Dynamics. Proc Natl Acad Sci U S A 104: 796-801.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 796-801
-
-
Rueda, M.1
Ferrer, C.2
Meyer, T.3
Pérez, A.4
Camps, J.5
-
86
-
-
78149459697
-
MoDEL (Molecular Dynamics Extended Library). A database of atomistic molecular dynamics simulations
-
Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, et al. (2010) MoDEL (Molecular Dynamics Extended Library). A database of atomistic molecular dynamics simulations. Structure 18: 1399-1409.
-
(2010)
Structure
, vol.18
, pp. 1399-1409
-
-
Meyer, T.1
D'Abramo, M.2
Hospital, A.3
Rueda, M.4
Ferrer-Costa, C.5
-
87
-
-
0000722070
-
Spectral methods of characterizing protein conformation and conformational changes
-
Creighton TE, editor. Oxford: IRL Press
-
Schmid FX (1989) Spectral methods of characterizing protein conformation and conformational changes. In: Creighton TE, editor. Protein Structure: a Practical Approach. Oxford: IRL Press. pp 251-285.
-
(1989)
Protein Structure: A Practical Approach
, pp. 251-285
-
-
Schmid, F.X.1
-
88
-
-
79952476196
-
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences
-
Best RB, Mittal J, (2011) Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences. Proteins 79: 1318-1328.
-
(2011)
Proteins
, vol.79
, pp. 1318-1328
-
-
Best, R.B.1
Mittal, J.2
-
89
-
-
79961148664
-
The Native ensemble and folding of a protein molten-globule: functional consequence of downhill folding
-
Naganathan AN, Orozco M, (2011) The Native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. J Am Chem Soc 133: 12154-61.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 12154-12161
-
-
Naganathan, A.N.1
Orozco, M.2
-
90
-
-
78249249624
-
Multiple routes characterize the folding of a small DNA hairpin
-
Portella G, Orozco M, (2010) Multiple routes characterize the folding of a small DNA hairpin. Angew Chem Int Ed Eng 49: 7673-7676.
-
(2010)
Angew Chem Int Ed Eng
, vol.49
, pp. 7673-7676
-
-
Portella, G.1
Orozco, M.2
-
91
-
-
77954383580
-
Design and Structure of an Equilibrium Protein Folding Intermediate: A Hint into Dynamical Regions of Proteins
-
Ayuso-Tejedor S, Espinosa Angarica V, Bueno M, Campos LA, Abián O, et al. (2010) Design and Structure of an Equilibrium Protein Folding Intermediate: A Hint into Dynamical Regions of Proteins. J Mol Biol 400: 922-934.
-
(2010)
J Mol Biol
, vol.400
, pp. 922-934
-
-
Ayuso-Tejedor, S.1
Espinosa Angarica, V.2
Bueno, M.3
Campos, L.A.4
Abián, O.5
-
92
-
-
33746322440
-
Do Proteins with Similar Folds Have Similar Transition State Structures? A Diffuse Transition State of the 169 Residue Apoflavodoxin
-
Bueno M, Ayuso-Tejedor S, Sancho J, (2006) Do Proteins with Similar Folds Have Similar Transition State Structures? A Diffuse Transition State of the 169 Residue Apoflavodoxin. J Mol Biol 359: 813-824.
-
(2006)
J Mol Biol
, vol.359
, pp. 813-824
-
-
Bueno, M.1
Ayuso-Tejedor, S.2
Sancho, J.3
|