-
1
-
-
33846700040
-
Chemistry Nobel rich in structure
-
Seringhaus M., and Gerstein M. Chemistry Nobel rich in structure. Science 315 (2007) 40-41
-
(2007)
Science
, vol.315
, pp. 40-41
-
-
Seringhaus, M.1
Gerstein, M.2
-
2
-
-
21644447473
-
-
Editorial: So much more to know. Science 2005, 309:78-102.
-
-
-
-
3
-
-
0016411482
-
Experimental and theoretical aspects of protein folding
-
Anfinsen C.B., and Scheraga H.A. Experimental and theoretical aspects of protein folding. Adv Protein Chem 29 (1975) 205-300
-
(1975)
Adv Protein Chem
, vol.29
, pp. 205-300
-
-
Anfinsen, C.B.1
Scheraga, H.A.2
-
4
-
-
0032993447
-
Polymer principles and protein folding
-
Dill K.A. Polymer principles and protein folding. Protein Sci 8 (1999) 1166-1180
-
(1999)
Protein Sci
, vol.8
, pp. 1166-1180
-
-
Dill, K.A.1
-
6
-
-
23444436172
-
Protein design by binary patterning of polar and nonpolar amino acids
-
Kamtekar S., Schiffer J.M., Xiong H., Babik J.M., and Hecht M.H. Protein design by binary patterning of polar and nonpolar amino acids. Science 262 (1993) 1680-1685
-
(1993)
Science
, vol.262
, pp. 1680-1685
-
-
Kamtekar, S.1
Schiffer, J.M.2
Xiong, H.3
Babik, J.M.4
Hecht, M.H.5
-
8
-
-
33645513791
-
Combinatorial approaches to probe the sequence determinants of protein aggregation and amyloidogenicity
-
Using combinatorial methods, Hecht and co-workers show the key sequence features that are related to natural amyloid formation, which helps decode the mechanism of formation of amyloid fibrils.
-
Wurth C., Kim W., and Hecht M.H. Combinatorial approaches to probe the sequence determinants of protein aggregation and amyloidogenicity. Protein Pept Lett 13 (2006) 279-286. Using combinatorial methods, Hecht and co-workers show the key sequence features that are related to natural amyloid formation, which helps decode the mechanism of formation of amyloid fibrils.
-
(2006)
Protein Pept Lett
, vol.13
, pp. 279-286
-
-
Wurth, C.1
Kim, W.2
Hecht, M.H.3
-
10
-
-
23744462184
-
Folding a nonbiological polymer into a compact multihelical structure
-
Lee et al. have made 'foldamers' using a non-biological backbone, in this case, a peptoid chain (N-substituted glycine). They show that these chains, up to 60-mers, fold cooperatively into multihelix bundle structures.
-
Lee B.C., Zuckermann R.N., and Dill K.A. Folding a nonbiological polymer into a compact multihelical structure. J Am Chem Soc 127 (2005) 10999-11009. Lee et al. have made 'foldamers' using a non-biological backbone, in this case, a peptoid chain (N-substituted glycine). They show that these chains, up to 60-mers, fold cooperatively into multihelix bundle structures.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 10999-11009
-
-
Lee, B.C.1
Zuckermann, R.N.2
Dill, K.A.3
-
11
-
-
0037159195
-
Design of non-cysteine-containing antimicrobial beta-hairpins: structure-activity relationship studies with linear protegrin-1 analogues
-
Lai J.R., Huck B.R., Weisblum B., and Gellman S.H. Design of non-cysteine-containing antimicrobial beta-hairpins: structure-activity relationship studies with linear protegrin-1 analogues. Biochemistry 41 (2002) 12835-12842
-
(2002)
Biochemistry
, vol.41
, pp. 12835-12842
-
-
Lai, J.R.1
Huck, B.R.2
Weisblum, B.3
Gellman, S.H.4
-
12
-
-
0344928208
-
Helical peptoid mimics of lung surfactant protein C
-
Wu C.W., Seurynck S.L., Lee K.Y., and Barron A.E. Helical peptoid mimics of lung surfactant protein C. Chem Biol 10 (2003) 1057-1063
-
(2003)
Chem Biol
, vol.10
, pp. 1057-1063
-
-
Wu, C.W.1
Seurynck, S.L.2
Lee, K.Y.3
Barron, A.E.4
-
13
-
-
33646357930
-
Rational development of beta-peptide inhibitors of human cytomegalovirus entry
-
Gellman and colleagues have designed 'β-peptides' that can inhibit human cytomegalovirus (HCMV), a pervasive and significant pathogen, from entering cells, possibly leading to a new class of antiviral agent.
-
English E.P., Chumanov R.S., Gellman S.H., and Compton T. Rational development of beta-peptide inhibitors of human cytomegalovirus entry. J Biol Chem 281 (2006) 2661-2667. Gellman and colleagues have designed 'β-peptides' that can inhibit human cytomegalovirus (HCMV), a pervasive and significant pathogen, from entering cells, possibly leading to a new class of antiviral agent.
-
(2006)
J Biol Chem
, vol.281
, pp. 2661-2667
-
-
English, E.P.1
Chumanov, R.S.2
Gellman, S.H.3
Compton, T.4
-
14
-
-
33745109340
-
A peptidomimetic siRNA transfection reagent for highly effective gene silencing
-
RNAi might be important for the therapeutic silencing of deleterious genes. This research describes the design of a 'lipitoid', a cationic oligopeptoid-phospholipid conjugate, for the non-viral transfection of synthetic siRNA oligos in cell culture, as a possible safe non-toxic delivery vehicle.
-
Utku Y., Dehan E., Ouerfelli O., Piano F., Zuckermann R.N., Pagano M., and Kirshenbaum K. A peptidomimetic siRNA transfection reagent for highly effective gene silencing. Mol Biosyst 2 (2006) 312-317. RNAi might be important for the therapeutic silencing of deleterious genes. This research describes the design of a 'lipitoid', a cationic oligopeptoid-phospholipid conjugate, for the non-viral transfection of synthetic siRNA oligos in cell culture, as a possible safe non-toxic delivery vehicle.
-
(2006)
Mol Biosyst
, vol.2
, pp. 312-317
-
-
Utku, Y.1
Dehan, E.2
Ouerfelli, O.3
Piano, F.4
Zuckermann, R.N.5
Pagano, M.6
Kirshenbaum, K.7
-
15
-
-
3042655537
-
Computational design of a biologically active enzyme
-
-6 rate enhancements over the uncatalyzed reaction and are biologically active.
-
-6 rate enhancements over the uncatalyzed reaction and are biologically active.
-
(2004)
Science
, vol.304
, pp. 1967-1971
-
-
Dwyer, M.A.1
Looger, L.L.2
Hellinga, H.W.3
-
16
-
-
4143131151
-
De novo design of catalytic proteins
-
These authors designed a novel catalyst, a phenol oxidase, from first principles. The catalytic peptides were designed by varying the monomer sequences. The peptides self-assembled to bind metal ions at an active site.
-
Kaplan J., and DeGrado W.F. De novo design of catalytic proteins. Proc Natl Acad Sci USA 101 (2004) 11566-11570. These authors designed a novel catalyst, a phenol oxidase, from first principles. The catalytic peptides were designed by varying the monomer sequences. The peptides self-assembled to bind metal ions at an active site.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 11566-11570
-
-
Kaplan, J.1
DeGrado, W.F.2
-
17
-
-
33750963095
-
Combinatorial methods for small-molecule placement in computational enzyme design
-
Lassila J.K., Privett H.K., Allen B.D., and Mayo S.L. Combinatorial methods for small-molecule placement in computational enzyme design. Proc Natl Acad Sci USA 103 (2006) 16710-16715
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 16710-16715
-
-
Lassila, J.K.1
Privett, H.K.2
Allen, B.D.3
Mayo, S.L.4
-
19
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B., Dantas G., Ireton G.C., Varani G., Stoddard B.L., and Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 302 (2003) 1364-1368
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
20
-
-
33646365635
-
Rigorous performance evaluation in protein structure modelling and implications for computational biology
-
This excellent review summarizes achievements in protein structure prediction methods throughout the six CASP competitions and the current challenges that remain to be solved.
-
Moult J. Rigorous performance evaluation in protein structure modelling and implications for computational biology. Philos Trans R Soc Lond B Biol Sci 361 (2006) 453-458. This excellent review summarizes achievements in protein structure prediction methods throughout the six CASP competitions and the current challenges that remain to be solved.
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, pp. 453-458
-
-
Moult, J.1
-
21
-
-
30344447955
-
Assessment of predictions submitted for the CASP6 comparative modeling category
-
Tress M., Ezkurdia I., Grana O., Lopez G., and Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins 61 suppl 7 (2005) 27-45
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 27-45
-
-
Tress, M.1
Ezkurdia, I.2
Grana, O.3
Lopez, G.4
Valencia, A.5
-
22
-
-
33644874394
-
MODBASE: a database of annotated comparative protein structure models and associated resources
-
Pieper U., Eswar N., Davis F.P., Braberg H., Madhusudhan M.S., Rossi A., Marti-Renom M., Karchin R., Webb B.M., Eramian D., et al. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34 (2006) D291-D295
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Pieper, U.1
Eswar, N.2
Davis, F.P.3
Braberg, H.4
Madhusudhan, M.S.5
Rossi, A.6
Marti-Renom, M.7
Karchin, R.8
Webb, B.M.9
Eramian, D.10
-
23
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Baker and co-workers show that Rosetta, their very successful bioinformatics-based structure prediction method, has now advanced to the stage of high-resolution structure prediction (<1.5 Å) over entire protein structures, for small single-domain proteins.
-
Bradley P., Misura K.M., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871. Baker and co-workers show that Rosetta, their very successful bioinformatics-based structure prediction method, has now advanced to the stage of high-resolution structure prediction (<1.5 Å) over entire protein structures, for small single-domain proteins.
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.2
Baker, D.3
-
24
-
-
30344488120
-
TASSER: an automated method for the prediction of protein tertiary structures in CASP6
-
The TASSER method is a highly successful method of computational protein structure prediction based on template identification by threading and 3D structure assembly through the rearrangement of template fragments using database-derived potentials.
-
Zhang Y., Arakaki A.K., and Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 61 suppl 7 (2005) 91-98. The TASSER method is a highly successful method of computational protein structure prediction based on template identification by threading and 3D structure assembly through the rearrangement of template fragments using database-derived potentials.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
-
25
-
-
33646374430
-
Prediction and design of macromolecular structures and interactions
-
Baker D. Prediction and design of macromolecular structures and interactions. Philos Trans R Soc Lond B Biol Sci 361 (2006) 459-463
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, pp. 459-463
-
-
Baker, D.1
-
26
-
-
28444488355
-
Solving the membrane protein folding problem
-
Bowie J.U. Solving the membrane protein folding problem. Nature 438 (2005) 581-589
-
(2005)
Nature
, vol.438
, pp. 581-589
-
-
Bowie, J.U.1
-
27
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Mendez R., Leplae R., Lensink M.F., and Wodak S.J. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60 (2005) 150-169
-
(2005)
Proteins
, vol.60
, pp. 150-169
-
-
Mendez, R.1
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
28
-
-
33745190979
-
Revisiting the prediction of protein function at CASP6
-
Pellegrini-Calace M., Soro S., and Tramontano A. Revisiting the prediction of protein function at CASP6. FEBS J 273 (2006) 2977-2983
-
(2006)
FEBS J
, vol.273
, pp. 2977-2983
-
-
Pellegrini-Calace, M.1
Soro, S.2
Tramontano, A.3
-
29
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y., and Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 (1998) 740-744
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
30
-
-
0037934616
-
Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins
-
Pitera J.W., and Swope W. Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. Proc Natl Acad Sci USA 100 (2003) 7587-7592
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 7587-7592
-
-
Pitera, J.W.1
Swope, W.2
-
31
-
-
0036428782
-
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
-
Zagrovic B., Snow C.D., Shirts M.R., and Pande V.S. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol 323 (2002) 927-937
-
(2002)
J Mol Biol
, vol.323
, pp. 927-937
-
-
Zagrovic, B.1
Snow, C.D.2
Shirts, M.R.3
Pande, V.S.4
-
32
-
-
0038329308
-
Folding at the speed limit
-
Yang W.Y., and Gruebele M. Folding at the speed limit. Nature 423 (2003) 193-197
-
(2003)
Nature
, vol.423
, pp. 193-197
-
-
Yang, W.Y.1
Gruebele, M.2
-
33
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek A., Kellis Jr. J.T., Serrano L., and Fersht A.R. Mapping the transition state and pathway of protein folding by protein engineering. Nature 340 (1989) 122-126
-
(1989)
Nature
, vol.340
, pp. 122-126
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Fersht, A.R.4
-
34
-
-
10644261303
-
Differences in the folding transition state of ubiquitin indicated by φ{symbol} and ψ analyses
-
Sosnick T.R., Dothager R.S., and Krantz B.A. Differences in the folding transition state of ubiquitin indicated by φ{symbol} and ψ analyses. Proc Natl Acad Sci USA 101 (2004) 17377-17382
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 17377-17382
-
-
Sosnick, T.R.1
Dothager, R.S.2
Krantz, B.A.3
-
35
-
-
33745955427
-
Specificity of the initial collapse in the folding of the cold shock protein
-
Magg C., Kubelka J., Holtermann G., Haas E., and Schmid F.X. Specificity of the initial collapse in the folding of the cold shock protein. J Mol Biol 360 (2006) 1067-1080
-
(2006)
J Mol Biol
, vol.360
, pp. 1067-1080
-
-
Magg, C.1
Kubelka, J.2
Holtermann, G.3
Haas, E.4
Schmid, F.X.5
-
36
-
-
0037126290
-
Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
-
Schuler B., Lipman E.A., and Eaton W.A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419 (2002) 743-747
-
(2002)
Nature
, vol.419
, pp. 743-747
-
-
Schuler, B.1
Lipman, E.A.2
Eaton, W.A.3
-
37
-
-
16344382372
-
Protein folding: the stepwise assembly of foldon units
-
Maity H., Maity M., Krishna M.M., Mayne L., and Englander S.W. Protein folding: the stepwise assembly of foldon units. Proc Natl Acad Sci USA 102 (2005) 4741-4746
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4741-4746
-
-
Maity, H.1
Maity, M.2
Krishna, M.M.3
Mayne, L.4
Englander, S.W.5
-
38
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277 (1998) 985-994
-
(1998)
J Mol Biol
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
39
-
-
33845403686
-
Nanosecond folding dynamics of a three-stranded β-sheet
-
This study reports the stability and folding kinetics of one of the fastest-folding proteins: a three-stranded β sheet. It folds in around 140 ns at 35.0 °C.
-
Xu Y., Purkayastha P., and Gai F. Nanosecond folding dynamics of a three-stranded β-sheet. J Am Chem Soc 128 (2006) 15836-15842. This study reports the stability and folding kinetics of one of the fastest-folding proteins: a three-stranded β sheet. It folds in around 140 ns at 35.0 °C.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 15836-15842
-
-
Xu, Y.1
Purkayastha, P.2
Gai, F.3
-
41
-
-
33746102627
-
Atom-by-atom analysis of global downhill protein folding
-
Sadqi M., Fushman D., and Munoz V. Atom-by-atom analysis of global downhill protein folding. Nature 442 (2006) 317-321
-
(2006)
Nature
, vol.442
, pp. 317-321
-
-
Sadqi, M.1
Fushman, D.2
Munoz, V.3
-
42
-
-
33846073474
-
Distinguishing between cooperative and unimodal downhill protein folding
-
Huang F., Sato S., Sharpe T.D., Ying L., and Fersht A.R. Distinguishing between cooperative and unimodal downhill protein folding. Proc Natl Acad Sci USA 104 (2007) 123-127
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 123-127
-
-
Huang, F.1
Sato, S.2
Sharpe, T.D.3
Ying, L.4
Fersht, A.R.5
-
43
-
-
0022423920
-
Theory for the folding and stability of globular proteins
-
Dill K.A. Theory for the folding and stability of globular proteins. Biochemistry 24 (1985) 1501-1509
-
(1985)
Biochemistry
, vol.24
, pp. 1501-1509
-
-
Dill, K.A.1
-
44
-
-
0026723063
-
Protein folding funnels: a kinetic approach to the sequence-structure relationship
-
Leopold P.E., Montal M., and Onuchic J.N. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc Natl Acad Sci USA 89 (1992) 8721-8725
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 8721-8725
-
-
Leopold, P.E.1
Montal, M.2
Onuchic, J.N.3
-
45
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill K.A., and Chan H.S. From Levinthal to pathways to funnels. Nat Struct Biol 4 (1997) 10-19
-
(1997)
Nat Struct Biol
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
47
-
-
13444301037
-
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
-
Levy Y., Cho S.S., Onuchic J.N., and Wolynes P.G. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol 346 (2005) 1121-1145
-
(2005)
J Mol Biol
, vol.346
, pp. 1121-1145
-
-
Levy, Y.1
Cho, S.S.2
Onuchic, J.N.3
Wolynes, P.G.4
-
48
-
-
0034872511
-
Transition states and the meaning of φ{symbol}-values in protein folding kinetics
-
Ozkan S.B., Bahar I., and Dill K.A. Transition states and the meaning of φ{symbol}-values in protein folding kinetics. Nat Struct Biol 8 (2001) 765-769
-
(2001)
Nat Struct Biol
, vol.8
, pp. 765-769
-
-
Ozkan, S.B.1
Bahar, I.2
Dill, K.A.3
-
49
-
-
33846026304
-
Transition-states in protein folding kinetics: the structural interpretation of φ{symbol} values
-
Weikl T.R., and Dill K.A. Transition-states in protein folding kinetics: the structural interpretation of φ{symbol} values. J Mol Biol 365 (2007) 1578-1586
-
(2007)
J Mol Biol
, vol.365
, pp. 1578-1586
-
-
Weikl, T.R.1
Dill, K.A.2
-
50
-
-
33746823043
-
Coil-globule transition in the denatured state of a small protein
-
This single-molecule study characterizes the equilibrium coil-globule transition in the denatured state of the Ig-binding domain of protein L. Using FRET measurements of individual protein molecules, the radius of gyration of the protein at different denaturant concentration is determined. Analysis reveals that the fully collapsed state of the protein is only ∼10% larger than the folded state.
-
Sherman E., and Haran G. Coil-globule transition in the denatured state of a small protein. Proc Natl Acad Sci USA 103 (2006) 11539-11543. This single-molecule study characterizes the equilibrium coil-globule transition in the denatured state of the Ig-binding domain of protein L. Using FRET measurements of individual protein molecules, the radius of gyration of the protein at different denaturant concentration is determined. Analysis reveals that the fully collapsed state of the protein is only ∼10% larger than the folded state.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 11539-11543
-
-
Sherman, E.1
Haran, G.2
-
51
-
-
25444512161
-
Direct observation of the three-state folding of a single protein molecule
-
This work studies the unfolding and refolding of single ribonuclease H (RNase H) protein molecules, using optical tweezers. The study provides a direct single-molecule observation of an intermediate state.
-
Cecconi C., Shank E.A., Bustamante C., and Marqusee S. Direct observation of the three-state folding of a single protein molecule. Science 309 (2005) 2057-2060. This work studies the unfolding and refolding of single ribonuclease H (RNase H) protein molecules, using optical tweezers. The study provides a direct single-molecule observation of an intermediate state.
-
(2005)
Science
, vol.309
, pp. 2057-2060
-
-
Cecconi, C.1
Shank, E.A.2
Bustamante, C.3
Marqusee, S.4
-
52
-
-
34247382025
-
Long-time protein folding dynamics from short-time molecular dynamics simulations
-
Chodera J.D., Swope W.C., Pitera J.E., and Dill K.A. Long-time protein folding dynamics from short-time molecular dynamics simulations. Multiscale Model Simul 54 (2006) 1214-1226
-
(2006)
Multiscale Model Simul
, vol.54
, pp. 1214-1226
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.E.3
Dill, K.A.4
-
53
-
-
33748248896
-
Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece
-
This is a massive computational study of a small single-domain protein, the villin headpiece. Using large-scale distributed computing, all-atom explicit solvent molecular dynamics (MD) simulations are sampled up to 500 μs in the form of ten of thousands of independent MD trajectories. Long-timescale kinetics are then obtained by constructing Markov models from the MD trajectories.
-
Jayachandran G., Vishal V., and Pande V.S. Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J Chem Phys 124 (2006) 164902. This is a massive computational study of a small single-domain protein, the villin headpiece. Using large-scale distributed computing, all-atom explicit solvent molecular dynamics (MD) simulations are sampled up to 500 μs in the form of ten of thousands of independent MD trajectories. Long-timescale kinetics are then obtained by constructing Markov models from the MD trajectories.
-
(2006)
J Chem Phys
, vol.124
, pp. 164902
-
-
Jayachandran, G.1
Vishal, V.2
Pande, V.S.3
-
55
-
-
33845611519
-
Routes are trees: the parsing perspective on protein folding
-
Hockenmaier J., Joshi A.K., and Dill K.A. Routes are trees: the parsing perspective on protein folding. Proteins 66 (2007) 1-15
-
(2007)
Proteins
, vol.66
, pp. 1-15
-
-
Hockenmaier, J.1
Joshi, A.K.2
Dill, K.A.3
-
56
-
-
33847060477
-
Exploring zipping and assembly as a protein folding principle
-
Voelz V.A., and Dill K.A. Exploring zipping and assembly as a protein folding principle. Proteins 66 (2007) 877-888
-
(2007)
Proteins
, vol.66
, pp. 877-888
-
-
Voelz, V.A.1
Dill, K.A.2
-
57
-
-
34547551805
-
-
Ozkan SB, Wu GA, Chodera JD, Dill KA: Protein folding by zipping and assembly. Proc Natl Acad Sci USA 2007, in press.
-
-
-
-
58
-
-
33847324863
-
A natively unfolded yeast prion monomer adopts an ensemble of compact and fluctuating structures
-
A single-molecule FRET study of a yeast prion protein, giving the full folding time distribution function.
-
Mukhopadhyay S., Krishnan R., Lemke E.A., Lindquist S., and Deniz A.A. A natively unfolded yeast prion monomer adopts an ensemble of compact and fluctuating structures. Proc Natl Acad Sci USA 104 (2007) 2649-2654. A single-molecule FRET study of a yeast prion protein, giving the full folding time distribution function.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 2649-2654
-
-
Mukhopadhyay, S.1
Krishnan, R.2
Lemke, E.A.3
Lindquist, S.4
Deniz, A.A.5
-
59
-
-
34247639441
-
Folding free energy landscape of villin headpiece subdomain from molecular dynamic simulations
-
These authors show accurate folding of the 36-mer villin headpiece protein using a physical all-atom model with implicit solvent.
-
Lei H., Wu C., Liu H., and Duan Y. Folding free energy landscape of villin headpiece subdomain from molecular dynamic simulations. Proc Natl Acad Sci USA 104 (2007) 4925-4930. These authors show accurate folding of the 36-mer villin headpiece protein using a physical all-atom model with implicit solvent.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 4925-4930
-
-
Lei, H.1
Wu, C.2
Liu, H.3
Duan, Y.4
|