-
1
-
-
0027318513
-
Macromolecular crowding: biochemical, biophysical, and physiological consequences
-
7688609, .;:–
-
Zimmerman SB, Minton AP, Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct. 1993;22:27–65. 7688609
-
(1993)
Annu Rev Biophys Biomol Struct
, vol.22
, pp. 27-65
-
-
Zimmerman, S.B.1
Minton, A.P.2
-
2
-
-
84877069692
-
Effects of macromolecular crowding agents on protein folding in vitro and in silico
-
.;():–
-
Christiansen A, Wang Q, Cheung MS, Wittung-Stafshede P, Effects of macromolecular crowding agents on protein folding in vitro and in silico. Biophys Rev. 2013;5(2):137–45.
-
(2013)
Biophys Rev
, vol.5
, Issue.2
, pp. 137-145
-
-
Christiansen, A.1
Wang, Q.2
Cheung, M.S.3
Wittung-Stafshede, P.4
-
3
-
-
77951298407
-
Models of macromolecular crowding effects and the need for quantitative comparisons with experiment
-
20167475, .;():–
-
Elcock AH, Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol. 2010;20(2):196–206. doi: 10.1016/j.sbi.2010.01.00820167475
-
(2010)
Curr Opin Struct Biol
, vol.20
, Issue.2
, pp. 196-206
-
-
Elcock, A.H.1
-
4
-
-
84893395763
-
Denatured State Structural Property Determines Protein Stabilization by Macromolecular Crowding: A Thermodynamic and Structural Approach
-
24265729, .;():
-
Singh LR, Mittal S, Denatured State Structural Property Determines Protein Stabilization by Macromolecular Crowding: A Thermodynamic and Structural Approach. PLoS ONE. 2013Nov12;8(11):e78936. doi: 10.1371/journal.pone.007893624265729
-
(2013)
PLoS ONE
, vol.8
, Issue.11
, pp. e78936
-
-
Singh, L.R.1
Mittal, S.2
-
5
-
-
41049090929
-
Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences
-
.;():–
-
Zhou H-X, Rivas G, Minton AP, Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys. 2008;37(1):375–97.
-
(2008)
Annu Rev Biophys
, vol.37
, Issue.1
, pp. 375-397
-
-
Zhou, H.-X.1
Rivas, G.2
Minton, A.P.3
-
6
-
-
70349310244
-
Nonadditive effects of mixed crowding on protein stability
-
19408299, .;():–
-
Batra J, Xu K, Zhou H-X, Nonadditive effects of mixed crowding on protein stability. Proteins. 2009Oct;77(1):133–8. doi: 10.1002/prot.2242519408299
-
(2009)
Proteins
, vol.77
, Issue.1
, pp. 133-138
-
-
Batra, J.1
Xu, K.2
Zhou, H.-X.3
-
7
-
-
84903287318
-
Protein Stabilization by Macromolecular Crowding through Enthalpy Rather Than Entropy
-
24888734, .;():–
-
Senske M, Törk L, Born B, Havenith M, Herrmann C, Ebbinghaus S, Protein Stabilization by Macromolecular Crowding through Enthalpy Rather Than Entropy. J Am Chem Soc. 2014Jun25;136(25):9036–41. doi: 10.1021/ja503205y24888734
-
(2014)
J Am Chem Soc
, vol.136
, Issue.25
, pp. 9036-9041
-
-
Senske, M.1
Törk, L.2
Born, B.3
Havenith, M.4
Herrmann, C.5
Ebbinghaus, S.6
-
8
-
-
84921690155
-
Beyond the excluded volume effects: mechanistic complexity of the crowded milieu
-
.;():–
-
Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN, Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Mol Basel Switz. 2015Jan;20(1):1377–409.
-
(2015)
Mol Basel Switz
, vol.20
, Issue.1
, pp. 1377-1409
-
-
Kuznetsova, I.M.1
Zaslavsky, B.Y.2
Breydo, L.3
Turoverov, K.K.4
Uversky, V.N.5
-
9
-
-
84913554025
-
NMR studies of protein folding and binding in cells and cell-like environments
-
25479354, .;:–
-
Smith AE, Zhang Z, Pielak GJ, Li C, NMR studies of protein folding and binding in cells and cell-like environments. Curr Opin Struct Biol. 2015Feb;30:7–16. doi: 10.1016/j.sbi.2014.10.00425479354
-
(2015)
Curr Opin Struct Biol
, vol.30
, pp. 7-16
-
-
Smith, A.E.1
Zhang, Z.2
Pielak, G.J.3
Li, C.4
-
10
-
-
84911423809
-
Revisiting a dogma: the effect of volume exclusion in molecular crowding
-
25464122, .;:–
-
Politou A, Temussi PA, Revisiting a dogma: the effect of volume exclusion in molecular crowding. Curr Opin Struct Biol. 2015Feb;30:1–6. doi: 10.1016/j.sbi.2014.10.00525464122
-
(2015)
Curr Opin Struct Biol
, vol.30
, pp. 1-6
-
-
Politou, A.1
Temussi, P.A.2
-
11
-
-
84922632709
-
Quinary structure modulates protein stability in cells
-
25624496, .;():–
-
Monteith WB, Cohen RD, Smith AE, Guzman-Cisneros E, Pielak GJ, Quinary structure modulates protein stability in cells. Proc Natl Acad Sci. 2015Feb10;112(6):1739–42. doi: 10.1073/pnas.141741511225624496
-
(2015)
Proc Natl Acad Sci
, vol.112
, Issue.6
, pp. 1739-1742
-
-
Monteith, W.B.1
Cohen, R.D.2
Smith, A.E.3
Guzman-Cisneros, E.4
Pielak, G.J.5
-
12
-
-
84867377395
-
Macromolecular crowding and protein stability
-
22954326, .;:–
-
Wang Y, Sarkar M, Smith AE, Krois AS, Pielak GJ, Macromolecular crowding and protein stability. J Am Chem Soc. 2012;134:16614–8. doi: 10.1021/ja305300m22954326
-
(2012)
J Am Chem Soc
, vol.134
, pp. 16614-16618
-
-
Wang, Y.1
Sarkar, M.2
Smith, A.E.3
Krois, A.S.4
Pielak, G.J.5
-
13
-
-
84905652881
-
Residue level quantification of protein stability in living cells
-
25049396, .;():–
-
Monteith WB, Pielak GJ, Residue level quantification of protein stability in living cells. Proc Natl Acad Sci U S A. 2014Aug;111(31):11335–40. doi: 10.1073/pnas.140684511125049396
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, Issue.31
, pp. 11335-11340
-
-
Monteith, W.B.1
Pielak, G.J.2
-
14
-
-
84888376873
-
Impact of reconstituted cytosol on protein stability
-
24218610, .;():–
-
Sarkar M, Smith AE, Pielak GJ, Impact of reconstituted cytosol on protein stability. Proc Natl Acad Sci U S A. 2013Nov26;110(48):19342–7. doi: 10.1073/pnas.131267811024218610
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.48
, pp. 19342-19347
-
-
Sarkar, M.1
Smith, A.E.2
Pielak, G.J.3
-
15
-
-
84874843784
-
Reduced native state stability in crowded cellular environment due to protein-protein interactions
-
23402619, .;:–
-
Harada R, Tochio N, Kigawa T, Sugita Y, Feig M, Reduced native state stability in crowded cellular environment due to protein-protein interactions. J Am Chem Soc. 2013;135:3696–701. doi: 10.1021/ja312699223402619
-
(2013)
J Am Chem Soc
, vol.135
, pp. 3696-3701
-
-
Harada, R.1
Tochio, N.2
Kigawa, T.3
Sugita, Y.4
Feig, M.5
-
16
-
-
84878940937
-
A decade and a half of protein intrinsic disorder: biology still waits for physics
-
.;:–
-
Uversky VN, A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci Publ Protein Soc. 2013;22:693–724.
-
(2013)
Protein Sci Publ Protein Soc
, vol.22
, pp. 693-724
-
-
Uversky, V.N.1
-
17
-
-
84897513201
-
Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments
-
24639500, ..;():–
-
Soranno A, Koenig I, Borgia MB, Hofmann H, Zosel F, Nettels D, et al. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. Proc Natl Acad Sci U S A. 2014Apr1;111(13):4874–9. doi: 10.1073/pnas.132261111124639500
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, Issue.13
, pp. 4874-4879
-
-
Soranno, A.1
Koenig, I.2
Borgia, M.B.3
Hofmann, H.4
Zosel, F.5
Nettels, D.6
-
18
-
-
34548722169
-
Macromolecular crowding induces a molten globule state in the C-terminal domain of histone H1
-
17513371, .;():–
-
Roque A, Ponte I, Suau P, Macromolecular crowding induces a molten globule state in the C-terminal domain of histone H1. Biophys J. 2007Sep15;93(6):2170–7. 17513371
-
(2007)
Biophys J
, vol.93
, Issue.6
, pp. 2170-2177
-
-
Roque, A.1
Ponte, I.2
Suau, P.3
-
19
-
-
77955044557
-
Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state
-
20662522, .;():–
-
Hong J, Gierasch LM, Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state. J Am Chem Soc. 2010Aug4;132(30):10445–52. doi: 10.1021/ja103166y20662522
-
(2010)
J Am Chem Soc
, vol.132
, Issue.30
, pp. 10445-10452
-
-
Hong, J.1
Gierasch, L.M.2
-
20
-
-
79951841821
-
Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching
-
21320458, .;:–
-
Johansen D, Jeffries CMJ, Hammouda B, Trewhella J, Goldenberg DP, Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching. Biophys J. 2011;100:1120–8. doi: 10.1016/j.bpj.2011.01.02021320458
-
(2011)
Biophys J
, vol.100
, pp. 1120-1128
-
-
Johansen, D.1
Jeffries, C.M.J.2
Hammouda, B.3
Trewhella, J.4
Goldenberg, D.P.5
-
21
-
-
84886041821
-
Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins
-
.;()
-
Qin S, Zhou H-X, Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins. J Phys Chem Lett. 2013Oct17;4(20).
-
(2013)
J Phys Chem Lett
, vol.4
, Issue.20
-
-
Qin, S.1
Zhou, H.-X.2
-
22
-
-
84894427113
-
Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study
-
24559993, .;():–
-
Goldenberg DP, Argyle B, Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study. Biophys J. 2014Feb18;106(4):905–14. doi: 10.1016/j.bpj.2013.12.00324559993
-
(2014)
Biophys J
, vol.106
, Issue.4
, pp. 905-914
-
-
Goldenberg, D.P.1
Argyle, B.2
-
23
-
-
79959807835
-
Protein disorder prevails under crowded conditions
-
.;():–
-
Szasz CS, Alexa A, Toth K, Rakacs M, Langowski J, Tompa P, Protein disorder prevails under crowded conditions. Biochemistry (Mosc). 2011Jul5;50(26):5834–44.
-
(2011)
Biochemistry (Mosc)
, vol.50
, Issue.26
, pp. 5834-5844
-
-
Szasz, C.S.1
Alexa, A.2
Toth, K.3
Rakacs, M.4
Langowski, J.5
Tompa, P.6
-
24
-
-
84882248932
-
Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State and the Folded Calcium-Bound State of a Repeat in Toxin (RTX) Protein
-
23941183, .;:–
-
Sotomayor-Pérez A-C, Subrini O, Hessel A, Ladant D, Chenal A, Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State and the Folded Calcium-Bound State of a Repeat in Toxin (RTX) Protein. J Am Chem Soc. 2013;135:11929–34. doi: 10.1021/ja404790f23941183
-
(2013)
J Am Chem Soc
, vol.135
, pp. 11929-11934
-
-
Sotomayor-Pérez, A.-C.1
Subrini, O.2
Hessel, A.3
Ladant, D.4
Chenal, A.5
-
25
-
-
84883079994
-
In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-synuclein within E. coli cells
-
23991082, ..;():
-
Waudby CA, Camilloni C, Fitzpatrick AWP, Cabrita LD, Dobson CM, Vendruscolo M, et al. In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-synuclein within E. coli cells. PloS One. 2013;8(8):e72286. doi: 10.1371/journal.pone.007228623991082
-
(2013)
PloS One
, vol.8
, Issue.8
, pp. e72286
-
-
Waudby, C.A.1
Camilloni, C.2
Fitzpatrick, A.W.P.3
Cabrita, L.D.4
Dobson, C.M.5
Vendruscolo, M.6
-
26
-
-
84873527015
-
Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales
-
.;;():–
-
Schuler B, Hofmann H, Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales. Curr Opin Struct Biol. Elsevier Ltd; 2013;23(1):36–47.
-
(2013)
Curr Opin Struct Biol. Elsevier Ltd
, vol.23
, Issue.1
, pp. 36-47
-
-
Schuler, B.1
Hofmann, H.2
-
27
-
-
84858198890
-
Protein Crowding Affects Hydration Structure and Dynamics
-
22352398, .;():–
-
Harada R, Sugita Y, Feig M, Protein Crowding Affects Hydration Structure and Dynamics. J Am Chem Soc. 2012Mar14;134(10):4842–9. doi: 10.1021/ja211115q22352398
-
(2012)
J Am Chem Soc
, vol.134
, Issue.10
, pp. 4842-4849
-
-
Harada, R.1
Sugita, Y.2
Feig, M.3
-
28
-
-
84864254504
-
Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations
-
22429139, .;():–
-
Predeus AV, Gul S, Gopal SM, Feig M, Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations. J Phys Chem B. 2012Jul26;116(29):8610–20. doi: 10.1021/jp300129u22429139
-
(2012)
J Phys Chem B
, vol.116
, Issue.29
, pp. 8610-8620
-
-
Predeus, A.V.1
Gul, S.2
Gopal, S.M.3
Feig, M.4
-
29
-
-
84868120948
-
Multimolecule test-tube simulations of protein unfolding and aggregation
-
23091038, .;():–
-
McCully ME, Beck DAC, Daggett V, Multimolecule test-tube simulations of protein unfolding and aggregation. Proc Natl Acad Sci U S A. 2012Oct30;109(44):17851–6. doi: 10.1073/pnas.120180910923091038
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, Issue.44
, pp. 17851-17856
-
-
McCully, M.E.1
Beck, D.A.C.2
Daggett, V.3
-
30
-
-
79961148664
-
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding
-
21732676, .;:–
-
Naganathan AN, Orozco M, The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. J Am Chem Soc. 2011;133:12154–61. doi: 10.1021/ja204053n21732676
-
(2011)
J Am Chem Soc
, vol.133
, pp. 12154-12161
-
-
Naganathan, A.N.1
Orozco, M.2
-
31
-
-
77955442470
-
Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP
-
20616042, .;():–
-
Kjaergaard M, Teilum K, Poulsen FM, Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP. Proc Natl Acad Sci. 2010Jul13;107(28):12535–40. doi: 10.1073/pnas.100169310720616042
-
(2010)
Proc Natl Acad Sci
, vol.107
, Issue.28
, pp. 12535-12540
-
-
Kjaergaard, M.1
Teilum, K.2
Poulsen, F.M.3
-
32
-
-
77955099224
-
Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II?
-
.;:–
-
Kjaergaard M, Nø rholm A-B, Hendus-Altenburger R, Pedersen SF, Poulsen FM, Kragelund BB, Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II?Protein Sci Publ Protein Soc. 2010;19:1555–64.
-
(2010)
Protein Sci Publ Protein Soc
, vol.19
, pp. 1555-1564
-
-
Kjaergaard, M.1
Nø rholm, A.-B.2
Hendus-Altenburger, R.3
Pedersen, S.F.4
Poulsen, F.M.5
Kragelund, B.B.6
-
33
-
-
84880027489
-
Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix–Helix Interactions
-
23758617, .;():–
-
Iešmantavičius V, bing Jensen MR, Ozenne V, Blackledge M, Poulsen FM, Kjaergaard M, Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix–Helix Interactions. J Am Chem Soc. 2013;135(27):10155–63. doi: 10.1021/ja404553223758617
-
(2013)
J Am Chem Soc
, vol.135
, Issue.27
, pp. 10155-10163
-
-
Iešmantavičius, V.1
bing Jensen, M.R.2
Ozenne, V.3
Blackledge, M.4
Poulsen, F.M.5
Kjaergaard, M.6
-
34
-
-
84864581257
-
A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations
-
22829760, .;():
-
Knott M, Best RB, A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations. PLoS Comput Biol. 2012Jul19;8(7):e1002605. doi: 10.1371/journal.pcbi.100260522829760
-
(2012)
PLoS Comput Biol
, vol.8
, Issue.7
, pp. e1002605
-
-
Knott, M.1
Best, R.B.2
-
35
-
-
84874963976
-
A folded excited state of ligand-free nuclear coactivator binding domain (NCBD) underlies plasticity in ligand recognition
-
.;():–
-
Kjaergaard M, Andersen L, Nielsen LD, Teilum K, A folded excited state of ligand-free nuclear coactivator binding domain (NCBD) underlies plasticity in ligand recognition. Biochemistry (Mosc). 2013Mar12;52(10):1686–93.
-
(2013)
Biochemistry (Mosc)
, vol.52
, Issue.10
, pp. 1686-1693
-
-
Kjaergaard, M.1
Andersen, L.2
Nielsen, L.D.3
Teilum, K.4
-
36
-
-
84859396047
-
Is a Malleable Protein Necessarily Highly Dynamic? The Hydrophobic Core of the Nuclear Coactivator Binding Domain Is Well Ordered
-
22500763, .;():–
-
Kjaergaard M, Poulsen FM, Teilum K, Is a Malleable Protein Necessarily Highly Dynamic? The Hydrophobic Core of the Nuclear Coactivator Binding Domain Is Well Ordered. Biophys J. 2012Apr4;102(7):1627–35. doi: 10.1016/j.bpj.2012.02.01422500763
-
(2012)
Biophys J
, vol.102
, Issue.7
, pp. 1627-1635
-
-
Kjaergaard, M.1
Poulsen, F.M.2
Teilum, K.3
-
37
-
-
84893454221
-
Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding
-
.;–
-
Iešmantavičius V, Dogan J, Jemth P, Teilum K, Kjaergaard M, Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding. Angew Chem Int Ed Engl. 2014;1–5.
-
(2014)
Angew Chem Int Ed Engl
, pp. 1-5
-
-
Iešmantavičius, V.1
Dogan, J.2
Jemth, P.3
Teilum, K.4
Kjaergaard, M.5
-
38
-
-
84883780574
-
The transition state structure for coupled binding and folding of disordered protein domains
-
.[cited 2015 Jun 20];. Available from:
-
Dogan J, Mu X, Engström Å, Jemth P, The transition state structure for coupled binding and folding of disordered protein domains. Sci Rep [Internet]. 2013Jun25 [cited 2015 Jun 20];3. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691887/
-
(2013)
Sci Rep [Internet]
, vol.3
-
-
Dogan, J.1
Mu, X.2
Engström, Å.3
Jemth, P.4
-
39
-
-
0035188314
-
Sequence complexity of disordered protein
-
11093259, .;():–
-
Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK, Sequence complexity of disordered protein. Proteins. 2001Jan1;42(1):38–48. 11093259
-
(2001)
Proteins
, vol.42
, Issue.1
, pp. 38-48
-
-
Romero, P.1
Obradovic, Z.2
Li, X.3
Garner, E.C.4
Brown, C.J.5
Dunker, A.K.6
-
40
-
-
77955686807
-
Effects of proteins on protein diffusion
-
20560582, .;():–
-
Wang Y, Li C, Pielak GJ, Effects of proteins on protein diffusion. J Am Chem Soc. 2010Jul14;132(27):9392–7. doi: 10.1021/ja102296k20560582
-
(2010)
J Am Chem Soc
, vol.132
, Issue.27
, pp. 9392-9397
-
-
Wang, Y.1
Li, C.2
Pielak, G.J.3
-
41
-
-
77950792003
-
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
-
20221255, .;():
-
McGuffee SR, Elcock AH, Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm. PLoS Comput Biol. 2010Mar5;6(3):e1000694. doi: 10.1371/journal.pcbi.100069420221255
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.3
, pp. e1000694
-
-
McGuffee, S.R.1
Elcock, A.H.2
-
42
-
-
84855848788
-
Variable Interactions between Protein Crowders and Biomolecular Solutes are Important in Understanding Cellular Crowding
-
22117862, .;():–
-
Feig M, Sugita Y, Variable Interactions between Protein Crowders and Biomolecular Solutes are Important in Understanding Cellular Crowding. J Phys Chem B. 2012Jan12;116(1):599–605. doi: 10.1021/jp209302e22117862
-
(2012)
J Phys Chem B
, vol.116
, Issue.1
, pp. 599-605
-
-
Feig, M.1
Sugita, Y.2
-
43
-
-
48249124302
-
Crowding effects on diffusion in solutions and cells
-
18573081, .;:–
-
Dix JA, Verkman AS, Crowding effects on diffusion in solutions and cells. Annu Rev Biophys. 2008;37:247–63. doi: 10.1146/annurev.biophys.37.032807.12582418573081
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 247-263
-
-
Dix, J.A.1
Verkman, A.S.2
-
44
-
-
84885405882
-
Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other
-
.;():–
-
Andrews CT, Elcock AH, Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other. J Chem Theory Comput. 2013Oct8;9(10):4585–602.
-
(2013)
J Chem Theory Comput
, vol.9
, Issue.10
, pp. 4585-4602
-
-
Andrews, C.T.1
Elcock, A.H.2
-
45
-
-
70350292376
-
Post-reductionist protein science, or putting Humpty Dumpty back together again
-
19841622, .;():–
-
Gierasch LM, Gershenson A, Post-reductionist protein science, or putting Humpty Dumpty back together again. Nat Chem Biol. 2009Nov;5(11):774–7. doi: 10.1038/nchembio.24119841622
-
(2009)
Nat Chem Biol
, vol.5
, Issue.11
, pp. 774-777
-
-
Gierasch, L.M.1
Gershenson, A.2
-
46
-
-
84860456767
-
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
-
22437851, .;():–
-
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL, MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics. 2012May1;28(9):1278–9. doi: 10.1093/bioinformatics/bts13922437851
-
(2012)
Bioinformatics
, vol.28
, Issue.9
, pp. 1278-1279
-
-
Hospital, A.1
Andrio, P.2
Fenollosa, C.3
Cicin-Sain, D.4
Orozco, M.5
Gelpí, J.L.6
-
47
-
-
84875592758
-
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
-
..;:–
-
Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinforma Oxf Engl. 2013;29:845–54.
-
(2013)
Bioinforma Oxf Engl
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Páll, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
-
48
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
.;:–
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR, Molecular dynamics with coupling to an external bath. J Chem Phys. 1984Oct1;81:3684–90.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
49
-
-
84943502952
-
A molecular-dynamics method for simulations in the canonical ensemble. Mol. Phys. 52, 255–268
-
.;():–
-
Nosé S, Nosé S., A molecular-dynamics method for simulations in the canonical ensemble. Mol. Phys. 52, 255–268. Mol Phys. 1984;52(2):255–68.
-
(1984)
Mol Phys
, vol.52
, Issue.2
, pp. 255-268
-
-
Nosé, S.1
Nosé, S.2
-
50
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
.;():–
-
Hoover WG, Canonical dynamics: Equilibrium phase-space distributions. Phys Rev A. 1985Mar1;31(3):1695–7.
-
(1985)
Phys Rev A
, vol.31
, Issue.3
, pp. 1695-1697
-
-
Hoover, W.G.1
-
51
-
-
33846823909
-
Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
-
.;():–
-
Darden T, York D, Pedersen L, Particle mesh Ewald: An N log(N) method for Ewald sums in large systems. J Chem Phys. 1993Jun15;98(12):10089–92.
-
(1993)
J Chem Phys
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
52
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
.;():–
-
Ryckaert J-P, Ciccotti G, Berendsen HJ, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23(3):327–41.
-
(1977)
J Comput Phys
, vol.23
, Issue.3
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.3
-
53
-
-
77953513118
-
Improved side-chain torsion potentials for the Amber ff99SB protein force field
-
20408171, ..;():–
-
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010Jun;78(8):1950–8. doi: 10.1002/prot.2271120408171
-
(2010)
Proteins
, vol.78
, Issue.8
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
-
54
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
.;():–
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML, Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79(2):926–35.
-
(1983)
J Chem Phys
, vol.79
, Issue.2
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
55
-
-
40549088261
-
Modeling of aqueous poly(oxyethylene) solutions: 1. Atomistic simulations
-
18251534, .;():–
-
Fischer J, Paschek D, Geiger A, Sadowski G, Modeling of aqueous poly(oxyethylene) solutions: 1. Atomistic simulations. J Phys Chem B. 2008Feb28;112(8):2388–98. doi: 10.1021/jp076534518251534
-
(2008)
J Phys Chem B
, vol.112
, Issue.8
, pp. 2388-2398
-
-
Fischer, J.1
Paschek, D.2
Geiger, A.3
Sadowski, G.4
-
56
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
.;():–
-
Frishman D, Argos P, Knowledge-based protein secondary structure assignment. Proteins Struct Funct Bioinforma. 1995Dec1;23(4):566–79.
-
(1995)
Proteins Struct Funct Bioinforma
, vol.23
, Issue.4
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
57
-
-
0029878720
-
VMD: visual molecular dynamics
-
8744570, .;():–,–
-
Humphrey W, Dalke A, Schulten K, VMD: visual molecular dynamics. J Mol Graph. 1996Feb;14(1):33–8, 27–8. 8744570
-
(1996)
J Mol Graph
, vol.14
, Issue.1
, pp. 28-33
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
58
-
-
0033556236
-
Peptide Folding: When Simulation Meets Experiment
-
.;():–
-
Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE, Peptide Folding: When Simulation Meets Experiment. Angew Chem Int Ed. 1999Jan15;38(1–2):236–40.
-
(1999)
Angew Chem Int Ed
, vol.38
, Issue.1-2
, pp. 236-240
-
-
Daura, X.1
Gademann, K.2
Jaun, B.3
Seebach, D.4
van Gunsteren, W.F.5
Mark, A.E.6
-
60
-
-
0035828630
-
On the calculation of entropy from covariance matrices of the atomic fluctuations
-
.;():–
-
Andricioaei I, Karplus M, On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys. 2001Oct8;115(14):6289–92.
-
(2001)
J Chem Phys
, vol.115
, Issue.14
, pp. 6289-6292
-
-
Andricioaei, I.1
Karplus, M.2
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