-
1
-
-
0037686252
-
The present view of the mechanism of protein folding
-
Daggett V., Fersht A. The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 4(6):2003;497-502.
-
(2003)
Nat. Rev. Mol. Cell Biol.
, vol.4
, Issue.6
, pp. 497-502
-
-
Daggett, V.1
Fersht, A.2
-
2
-
-
0037221599
-
Is there a unifying mechanism for protein folding?
-
Daggett V., Fersht A.R. Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28(1):2003;18-25.
-
(2003)
Trends Biochem. Sci.
, vol.28
, Issue.1
, pp. 18-25
-
-
Daggett, V.1
Fersht, A.R.2
-
3
-
-
0033624685
-
Fast kinetics and mechanisms in protein folding
-
Eaton W.A., Munoz V., Hagen S.J., Jas G.S., Lapidus L.J., Henry E.R., Hofrichter J. Fast kinetics and mechanisms in protein folding. Annu. Rev. Biophys. Biomech. 29:2000;327-359.
-
(2000)
Annu. Rev. Biophys. Biomech.
, vol.29
, pp. 327-359
-
-
Eaton, W.A.1
Munoz, V.2
Hagen, S.J.3
Jas, G.S.4
Lapidus, L.J.5
Henry, E.R.6
Hofrichter, J.7
-
4
-
-
0031587288
-
Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variants in water
-
Mohanty D., Elber R., Thirumalai D., Beglov D., Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 272(3):1997;423-442.
-
(1997)
J. Mol. Biol.
, vol.272
, Issue.3
, pp. 423-442
-
-
Mohanty, D.1
Elber, R.2
Thirumalai, D.3
Beglov, D.4
Roux, B.5
-
5
-
-
0034324530
-
Probing the role of local propensity in peptide turn formation
-
Mohanty D., Elber R., Thirumalai D. Probing the role of local propensity in peptide turn formation. Int. J. Quantum. Chem. 80(4/5):2000;1125-1128.
-
(2000)
Int. J. Quantum. Chem.
, vol.80
, Issue.4-5
, pp. 1125-1128
-
-
Mohanty, D.1
Elber, R.2
Thirumalai, D.3
-
6
-
-
0034710426
-
Folding studies of a linear pentamer peptide adopting a reverse turn conformation in aqueous solution through molecular dynamics simulation
-
Wu X.W., Wang S.M. Folding studies of a linear pentamer peptide adopting a reverse turn conformation in aqueous solution through molecular dynamics simulation. J. Phys. Chem. B. 104(33):2000;8023-8034.
-
(2000)
J. Phys. Chem. B.
, vol.104
, Issue.33
, pp. 8023-8034
-
-
Wu, X.W.1
Wang, S.M.2
-
7
-
-
0035179018
-
Helix nucleation kinetics from molecular simulations in explicit solvent
-
Hummer G., Garcia A.E., Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins. 42(1):2001;77-84.
-
(2001)
Proteins
, vol.42
, Issue.1
, pp. 77-84
-
-
Hummer, G.1
Garcia, A.E.2
Garde, S.3
-
8
-
-
0032584783
-
Reversible peptide folding in solution by molecular dynamics simulation
-
Daura X., Jaun B., Seebach D., van Gunsteren W.F., Mark A.E. Reversible peptide folding in solution by molecular dynamics simulation. J. Mol. Biol. 280(5):1998;925-932.
-
(1998)
J. Mol. Biol.
, vol.280
, Issue.5
, pp. 925-932
-
-
Daura, X.1
Jaun, B.2
Seebach, D.3
Van Gunsteren, W.F.4
Mark, A.E.5
-
9
-
-
0032800402
-
The effect of motional averaging on the calculation of nmr-derived structural properties
-
Daura X., Antes I., van Gunsteren W.F., Thiel W., Mark A.E. The effect of motional averaging on the calculation of nmr-derived structural properties. Proteins. 36(4):1999;542-555.
-
(1999)
Proteins
, vol.36
, Issue.4
, pp. 542-555
-
-
Daura, X.1
Antes, I.2
Van Gunsteren, W.F.3
Thiel, W.4
Mark, A.E.5
-
10
-
-
0035932703
-
Helix folding of an alanine-based peptide in explicit water
-
Wu X.W., Wang S.M. Helix folding of an alanine-based peptide in explicit water. J. Phys. Chem. B. 105(11):2001;2227-2235.
-
(2001)
J. Phys. Chem. B.
, vol.105
, Issue.11
, pp. 2227-2235
-
-
Wu, X.W.1
Wang, S.M.2
-
11
-
-
0034806777
-
The beta-peptide hairpin in solution: Conformational study of a beta-hexapeptide in methanol by nmr spectroscopy and md simulation
-
Daura X., Gademann K., Schafer H., Jaun B., Seebach D., van Gunsteren W.F. The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by nmr spectroscopy and md simulation. J. Am. Chem. Soc. 123(10):2001;2393-2404.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, Issue.10
, pp. 2393-2404
-
-
Daura, X.1
Gademann, K.2
Schafer, H.3
Jaun, B.4
Seebach, D.5
Van Gunsteren, W.F.6
-
12
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y., Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282(5389):1998;740-744.
-
(1998)
Science
, vol.282
, Issue.5389
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
13
-
-
0032544002
-
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation
-
Duan Y., Wang L., Kollman P.A. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc. Natl. Acad. Sci. U.S.A. 95(17):1998;9897-9902.
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, Issue.17
, pp. 9897-9902
-
-
Duan, Y.1
Wang, L.2
Kollman, P.A.3
-
14
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T., Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288(3):1999;477-487.
-
(1999)
J. Mol. Biol.
, vol.288
, Issue.3
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
15
-
-
0036138028
-
Evaluation of a fast implicit solvent model for molecular dynamics simulations
-
Ferrara P., Apostolakis J., Caflisch A. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins. 46(1):2002;24-33.
-
(2002)
Proteins
, vol.46
, Issue.1
, pp. 24-33
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
16
-
-
0344778061
-
Semi-analytical treatment of solvation for molecular mechanics and dynamics
-
Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. Semi-analytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112:1990;6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
17
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel beta-sheet peptide
-
Ferrara P., Caflisch A. Folding simulations of a three-stranded antiparallel beta-sheet peptide. Proc. Natl. Acad. Sci. U.S.A. 97(20):2000;10780-10785.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, Issue.20
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
18
-
-
0034324385
-
Free energy surface of the helical peptide y(meara)(6)
-
Hiltpold A., Ferrara P., Gsponer J., Caflisch A. Free energy surface of the helical peptide y(meara)(6). J. Phys. Chem. B. 104(43):2000;10080-10086.
-
(2000)
J. Phys. Chem. B.
, vol.104
, Issue.43
, pp. 10080-10086
-
-
Hiltpold, A.1
Ferrara, P.2
Gsponer, J.3
Caflisch, A.4
-
19
-
-
0036394906
-
Native-like mean structure in the unfolded ensemble of small proteins
-
Zagrovic B., Snow C.D., Khaliq S., Shirts M.R., Pande V.S. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323(1):2002;153-164.
-
(2002)
J. Mol. Biol.
, vol.323
, Issue.1
, pp. 153-164
-
-
Zagrovic, B.1
Snow, C.D.2
Khaliq, S.3
Shirts, M.R.4
Pande, V.S.5
-
20
-
-
0037470691
-
Ab initio folding simulation of the trp-cage mini-protein approaches nmr resolution
-
Chowdhury S., Lee M.C., Xiong G.M., Duan Y. Ab initio folding simulation of the trp-cage mini-protein approaches nmr resolution. J. Mol. Biol. 327(3):2003;711-717.
-
(2003)
J. Mol. Biol.
, vol.327
, Issue.3
, pp. 711-717
-
-
Chowdhury, S.1
Lee, M.C.2
Xiong, G.M.3
Duan, Y.4
-
21
-
-
0001767031
-
Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
-
Ferrara P., Apostolakis J., Caflisch A. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B. 104(20):2000;5000-5010.
-
(2000)
J. Phys. Chem. B.
, vol.104
, Issue.20
, pp. 5000-5010
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
22
-
-
0033022072
-
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures
-
Wang L., Duan Y., Shortle R., Imperiali B., Kollman P.A. Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. Protein Sci. 8(6):1999;1292-1304.
-
(1999)
Protein Sci.
, vol.8
, Issue.6
, pp. 1292-1304
-
-
Wang, L.1
Duan, Y.2
Shortle, R.3
Imperiali, B.4
Kollman, P.A.5
-
23
-
-
0034620730
-
Molecular dynamics simulations of three-strand beta-sheet folding
-
Wang H.W., Sung S.S. Molecular dynamics simulations of three-strand beta-sheet folding. J. Am. Chem. Soc. 122(9):2000;1999-2009.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, Issue.9
, pp. 1999-2009
-
-
Wang, H.W.1
Sung, S.S.2
-
24
-
-
0035793713
-
Native topology or specific interactions. What is more important for protein folding?
-
Ferrara P., Caflisch A. Native topology or specific interactions. What is more important for protein folding? J. Mol. Biol. 306(4):2001;837-850.
-
(2001)
J. Mol. Biol.
, vol.306
, Issue.4
, pp. 837-850
-
-
Ferrara, P.1
Caflisch, A.2
-
25
-
-
0035850758
-
Beta-hairpin folding simulations in atomistic detail using an implicit solvent model
-
Zagrovic B., Sorin E.J., Pande V. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313(1):2001;151-169.
-
(2001)
J. Mol. Biol.
, vol.313
, Issue.1
, pp. 151-169
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.3
-
26
-
-
0037042264
-
Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif
-
Jang S., Shin S., Pak Y. Molecular dynamics study of peptides in implicit water: ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif. J. Am. Chem. Soc. 124(18):2002;4976-4977.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, Issue.18
, pp. 4976-4977
-
-
Jang, S.1
Shin, S.2
Pak, Y.3
-
27
-
-
0037093655
-
Weak temperature dependence of the free energy surface and folding pathways of structured peptides
-
Cavalli A., Ferrara P., Caflisch A. Weak temperature dependence of the free energy surface and folding pathways of structured peptides. Proteins. 47(3):2002;305-314.
-
(2002)
Proteins
, vol.47
, Issue.3
, pp. 305-314
-
-
Cavalli, A.1
Ferrara, P.2
Caflisch, A.3
-
28
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling C., Strockbine B., Roitberg A.E. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124(38):2002;11258-11259.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, Issue.38
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
29
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow C.D., Nguyen N., Pande V.S., Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 420(6911):2002;102-106.
-
(2002)
Nature
, vol.420
, Issue.6911
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, N.2
Pande, V.S.3
Gruebele, M.4
-
30
-
-
0037065310
-
The trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
-
Snow C.D., Zagrovic B., Pande V.S. The trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. J. Am. Chem. Soc. 124(49):2002;14548-14549.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, Issue.49
, pp. 14548-14549
-
-
Snow, C.D.1
Zagrovic, B.2
Pande, V.S.3
-
31
-
-
0037934616
-
Understanding folding and design: Replica-exchange simulations of "trp-cage" miniproteins
-
Pitera J.W., Swope W. Understanding folding and design: replica-exchange simulations of "trp-cage" miniproteins. PNAS. 100(13):2003;7587-7592.
-
(2003)
PNAS
, vol.100
, Issue.13
, pp. 7587-7592
-
-
Pitera, J.W.1
Swope, W.2
-
32
-
-
0035703089
-
Rosetta in CASP4: Progress in ab initio protein structure prediction
-
Bonneau R., Tsai J., Ruczinski I., Chivian D., Rohl C., Strauss C.E.M., Baker D. Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. 45(S5):2001;119-126.
-
(2001)
Proteins
, vol.45
, Issue.S5
, pp. 119-126
-
-
Bonneau, R.1
Tsai, J.2
Ruczinski, I.3
Chivian, D.4
Rohl, C.5
Strauss, C.E.M.6
Baker, D.7
-
33
-
-
0036137805
-
Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, amber energy functions, and a generalized born/solvent accessibility solvation model
-
Liu Y.X., Beveridge D.L. Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, amber energy functions, and a generalized born/solvent accessibility solvation model. Proteins. 46(1):2002;128-146.
-
(2002)
Proteins
, vol.46
, Issue.1
, pp. 128-146
-
-
Liu, Y.X.1
Beveridge, D.L.2
-
34
-
-
0032606133
-
Ab initio protein structure prediction using a combined hierarchical approach
-
Samudrala R., Xia Y., Huang E., Levitt M. Ab initio protein structure prediction using a combined hierarchical approach. Proteins. 37(S3):1999;194-198.
-
(1999)
Proteins
, vol.37
, Issue.S3
, pp. 194-198
-
-
Samudrala, R.1
Xia, Y.2
Huang, E.3
Levitt, M.4
-
35
-
-
0032620117
-
Improved ab initio predictions with a simplified, flexible geometry model
-
Osguthorpe D.J. Improved ab initio predictions with a simplified, flexible geometry model. Proteins. 37(S3):1999;186-193.
-
(1999)
Proteins
, vol.37
, Issue.S3
, pp. 186-193
-
-
Osguthorpe, D.J.1
-
36
-
-
0001031117
-
Application of the diffusion equation method of global optimization to water clusters
-
Wawak R.J., Wimmer M.M., Scheraga H.A. Application of the diffusion equation method of global optimization to water clusters. J. Phys. Chem. (US). 96(12):1992;5138-5145.
-
(1992)
J. Phys. Chem. (US)
, vol.96
, Issue.12
, pp. 5138-5145
-
-
Wawak, R.J.1
Wimmer, M.M.2
Scheraga, H.A.3
-
37
-
-
0001031118
-
Application of the diffusion equation method for global optimization to oligopeptides
-
Kostrowicki J., Scheraga H.A. Application of the diffusion equation method for global optimization to oligopeptides. J. Phys. Chem. (US). 96(18):1992;7442-7449.
-
(1992)
J. Phys. Chem. (US)
, vol.96
, Issue.18
, pp. 7442-7449
-
-
Kostrowicki, J.1
Scheraga, H.A.2
-
38
-
-
0031211551
-
Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics
-
Huber T., Torda A.E., vanGunsteren W.F. Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics. J. Phys. Chem. A. 101(33):1997;5926-5930.
-
(1997)
J. Phys. Chem. a
, vol.101
, Issue.33
, pp. 5926-5930
-
-
Huber, T.1
Torda, A.E.2
Vangunsteren, W.F.3
-
39
-
-
0032932375
-
A potential smoothing algorithm accurately predicts transmembrane helix packing
-
Pappu R.V., Marshall G.R., Ponder J.W. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat. Struct. Biol. 6(1):1999;50-55.
-
(1999)
Nat. Struct. Biol.
, vol.6
, Issue.1
, pp. 50-55
-
-
Pappu, R.V.1
Marshall, G.R.2
Ponder, J.W.3
-
40
-
-
0029869187
-
Mean-field minimization methods for biological macromolecules
-
Koehl P., Delarue M. Mean-field minimization methods for biological macromolecules. Curr. Opin. Struct. Biol. 6(2):1996;222-226.
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, Issue.2
, pp. 222-226
-
-
Koehl, P.1
Delarue, M.2
-
41
-
-
36449006131
-
Modeling side-chains in peptides and proteins - Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
-
Roitberg A., Elber R. Modeling side-chains in peptides and proteins - application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations. J. Chem. Phys. 95(12):1991;9277-9287.
-
(1991)
J. Chem. Phys.
, vol.95
, Issue.12
, pp. 9277-9287
-
-
Roitberg, A.1
Elber, R.2
-
42
-
-
0032540692
-
Use of locally enhanced sampling in free energy calculations: Testing and application to the alpha→beta anomerization of glucose
-
Simmerling C., Fox T., Kollman P.A. Use of locally enhanced sampling in free energy calculations: testing and application to the alpha→beta anomerization of glucose. J. Am. Chem. Soc. 120(23):1998;5771-5782.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, Issue.23
, pp. 5771-5782
-
-
Simmerling, C.1
Fox, T.2
Kollman, P.A.3
-
43
-
-
0032578192
-
Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a non-helical nucleic acid
-
Simmerling C., Miller J.L., Kollman P.A. Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a non-helical nucleic acid. J. Am. Chem. Soc. 120(29):1998;7149- 7155.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, Issue.29
, pp. 7149-7155
-
-
Simmerling, C.1
Miller, J.L.2
Kollman, P.A.3
-
44
-
-
0033828425
-
Combining MONSSTER and LES/PME to predict protein structure from amino acid sequence: Application to the small protein CMTI-1
-
Simmerling C., Lee M.R., Ortiz A.R., Kolinski A., Skolnick J., Kollman P.A. Combining MONSSTER and LES/PME to predict protein structure from amino acid sequence: application to the small protein CMTI-1. J. Am. Chem. Soc. 122(35):2000;8392-8402.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, Issue.35
, pp. 8392-8402
-
-
Simmerling, C.1
Lee, M.R.2
Ortiz, A.R.3
Kolinski, A.4
Skolnick, J.5
Kollman, P.A.6
-
45
-
-
0033117917
-
New Monte Carlo algorithms for protein folding
-
Hansmann U.H.E., Okamoto Y. New Monte Carlo algorithms for protein folding. Curr. Opin. Struct. Biol. 9(2):1999;177-183.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, Issue.2
, pp. 177-183
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
-
46
-
-
0035749546
-
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement
-
Skolnick J., Kolinski A., Kihara D., Betancourt M., Rotkiewicz P., Boniecki M. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins. 45(S5):2001;149-156.
-
(2001)
Proteins
, vol.45
, Issue.S5
, pp. 149-156
-
-
Skolnick, J.1
Kolinski, A.2
Kihara, D.3
Betancourt, M.4
Rotkiewicz, P.5
Boniecki, M.6
-
47
-
-
0000515108
-
Self-guided molecular dynamics simulation for efficient conformational search
-
Wu X.W., Wang S.M. Self-guided molecular dynamics simulation for efficient conformational search. J. Phys. Chem. B. 102(37):1998;7238-7250.
-
(1998)
J. Phys. Chem. B.
, vol.102
, Issue.37
, pp. 7238-7250
-
-
Wu, X.W.1
Wang, S.M.2
-
48
-
-
0032607091
-
Enhanced systematic motion in molecular dynamics simulation
-
Wu X.W., Wang S.M. Enhanced systematic motion in molecular dynamics simulation. J. Chem. Phys. 110:1999;9401-9410.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 9401-9410
-
-
Wu, X.W.1
Wang, S.M.2
-
49
-
-
0037439853
-
Self-guided enhanced sampling methods for thermodynamic averages
-
Andricioaei I., Dinner A.R., Karplus M. Self-guided enhanced sampling methods for thermodynamic averages. J. Chem. Phys. 118(3):2003;1074-1084.
-
(2003)
J. Chem. Phys.
, vol.118
, Issue.3
, pp. 1074-1084
-
-
Andricioaei, I.1
Dinner, A.R.2
Karplus, M.3
-
50
-
-
0242509772
-
Self-guided Langevin dynamics method
-
Wu X.W., Brooks B.R. Self-guided Langevin dynamics method. Chem. Phys. Lett. 381(3-4):2003;512-518.
-
(2003)
Chem. Phys. Lett.
, vol.381
, Issue.34
, pp. 512-518
-
-
Wu, X.W.1
Brooks, B.R.2
-
51
-
-
0033064123
-
Unrestrained stochastic dynamics simulations of the uucg tetraloop using an implicit solvation model
-
Williams D.J., Hall K.B. Unrestrained stochastic dynamics simulations of the uucg tetraloop using an implicit solvation model. Biophys. J. 76(6):1999;3192-3205.
-
(1999)
Biophys. J.
, vol.76
, Issue.6
, pp. 3192-3205
-
-
Williams, D.J.1
Hall, K.B.2
-
52
-
-
0035132373
-
A new twist on the helix-coil transition: A non-biological helix with protein-like intermediates and traps
-
Elmer S., Pande V.S. A new twist on the helix-coil transition: a non-biological helix with protein-like intermediates and traps. J. Phys. Chem. B. 105(2):2001;482-485.
-
(2001)
J. Phys. Chem. B
, vol.105
, Issue.2
, pp. 482-485
-
-
Elmer, S.1
Pande, V.S.2
-
53
-
-
0036771626
-
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
-
Luo R., David L., Gilson M.K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem. 23:2002;1244-1253.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
54
-
-
0347410858
-
A Poisson-Boltzmann dynamics method with the non-periodic boundary condition
-
Lu J.Q., Luo R. A Poisson-Boltzmann dynamics method with the non-periodic boundary condition. J. Chem. Phys. 119(21):2003;11035-11047.
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.21
, pp. 11035-11047
-
-
Lu, J.Q.1
Luo, R.2
-
56
-
-
0030567375
-
Economy in protein design: Evolution of a metal-independent beta beta alpha motif based on the zinc finger domains
-
Struthers M.D., Cheng R.P., Imperiali B. Economy in protein design: evolution of a metal-independent beta beta alpha motif based on the zinc finger domains. J. Am. Chem. Soc. 118(13):1996;3073-3081.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, Issue.13
, pp. 3073-3081
-
-
Struthers, M.D.1
Cheng, R.P.2
Imperiali, B.3
-
57
-
-
0008501653
-
A thermostable 35-residue subdomain within villin headpiece
-
McKnight C.J., Doering D.S., Matsudaira P.T., Kim P.S. A thermostable 35-residue subdomain within villin headpiece. J. Mol. Biol. 260(2):1996;126-134.
-
(1996)
J. Mol. Biol.
, vol.260
, Issue.2
, pp. 126-134
-
-
McKnight, C.J.1
Doering, D.S.2
Matsudaira, P.T.3
Kim, P.S.4
-
58
-
-
0031058410
-
Nmr structure of the 35-residue villin headpiece subdomain
-
McKnight C.J., Matsudaira P.T., Kim P.S. Nmr structure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 4(3):1997;180-184.
-
(1997)
Nat. Struct. Biol.
, vol.4
, Issue.3
, pp. 180-184
-
-
McKnight, C.J.1
Matsudaira, P.T.2
Kim, P.S.3
-
59
-
-
0035107570
-
Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex
-
Lee L.P., Tidor B. Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex. Protein Sci. 10(2):2001;362-377.
-
(2001)
Protein Sci.
, vol.10
, Issue.2
, pp. 362-377
-
-
Lee, L.P.1
Tidor, B.2
-
60
-
-
1942452222
-
A physical scoring function based on the AMBER force field and the Poisson-Boltzmann implicit solvent for protein structure prediction
-
submitted.
-
M.J. Hsieh, R. Luo, A physical scoring function based on the AMBER force field and the Poisson-Boltzmann implicit solvent for protein structure prediction, Proteins, submitted.
-
Proteins
-
-
Hsieh, M.J.1
Luo, R.2
-
61
-
-
33846823909
-
Particle mesh Ewald - An nlog(n) method for Ewald sums in large systems
-
Darden T., York D., Pedersen L. Particle mesh Ewald - an nlog(n) method for Ewald sums in large systems. J. Chem. Phys. 98(12):1993;10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
62
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J. Am. Chem. Soc. 117(19):1995;5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, Issue.19
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
63
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:1984;3684-3690.
-
(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
-
66
-
-
22944467757
-
Computer experiments on classical fluids. Part i: Thermodynamical properties of Lennard-Jones molecules
-
Verlet L. Computer experiments on classical fluids. Part i: Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159(1):1967;98-100.
-
(1967)
Phys. Rev.
, vol.159
, Issue.1
, pp. 98-100
-
-
Verlet, L.1
-
68
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvation models
-
Sitkoff D., Sharp K.A., Honig B. Accurate calculation of hydration free energies using macroscopic solvation models. J. Phys. Chem. 98:1994;1978-1988.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
69
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.8
-
71
-
-
0020997912
-
Dictionary of protein secondary structure - Pattern-recognition of hydrogen-bonded and geometrical features
-
Kabsch W., Sander C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers. 22(12):1983;2577-2637.
-
(1983)
Biopolymers
, vol.22
, Issue.12
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
72
-
-
0024417964
-
The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure
-
Kuwajima K. The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins. 6(2):1989;87-103.
-
(1989)
Proteins
, vol.6
, Issue.2
, pp. 87-103
-
-
Kuwajima, K.1
-
73
-
-
0034724174
-
Effect of an alternative disulfide bond on the structure, stability, and folding of human lysozyme
-
Arai M., Hamel P., Kanaya E., Inaka K., Miki K., Kikuchi M., Kuwajima K. Effect of an alternative disulfide bond on the structure, stability, and folding of human lysozyme. Biochemistry (US). 39(12):2000;3472-3479.
-
(2000)
Biochemistry (US)
, vol.39
, Issue.12
, pp. 3472-3479
-
-
Arai, M.1
Hamel, P.2
Kanaya, E.3
Inaka, K.4
Miki, K.5
Kikuchi, M.6
Kuwajima, K.7
|