-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
-
(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
-
3
-
-
0033954256
-
The protein data bank
-
Herman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The protein data bank. Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Herman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
4
-
-
0030853453
-
Polyalanine-based peptides as models for self-associated β-pleated-sheet complexes
-
Blondelle, S. E., B. Forood, R. A. Houghten, and E. Pérez- Payá. 1997. Polyalanine-based peptides as models for self-associated β-pleated-sheet complexes. Biochemistry. 36:8393-8400.
-
(1997)
Biochemistry
, vol.36
, pp. 8393-8400
-
-
Blondelle, S.E.1
Forood, B.2
Houghten, R.A.3
Pérez-Payá, E.4
-
5
-
-
0037551741
-
Protofibrils, pores, fibrils, and neurodegeneration: Separating the responsible protein aggregates from the innocent bystanders
-
Caughey, B., and P. T. Lansbury, Jr. 2003. Protofibrils, pores, fibrils, and neurodegeneration: Separating the responsible protein aggregates from the innocent bystanders. Annu. Rev. Neurosci. 26:267-298.
-
(2003)
Annu. Rev. Neurosci.
, vol.26
, pp. 267-298
-
-
Caughey, B.1
Lansbury Jr., P.T.2
-
6
-
-
0025804130
-
Large differences in the helix propensities of alanine and glycine
-
Chakrabartty, A., J. Schellman, and R. Baldwin. 1991. Large differences in the helix propensities of alanine and glycine. Nature. 351:586-588.
-
(1991)
Nature
, vol.351
, pp. 586-588
-
-
Chakrabartty, A.1
Schellman, J.2
Baldwin, R.3
-
7
-
-
0035800572
-
Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity
-
Chen, S., V. Berthelier, W. Yang, and R. Wetzel. 2001. Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity. J. Mol. Biol. 311:173-182.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 173-182
-
-
Chen, S.1
Berthelier, V.2
Yang, W.3
Wetzel, R.4
-
8
-
-
0037015081
-
Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation
-
Chen, S., F. A. Ferrone, and R. Wetzel. 2002. Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation. Proc. Natl. Acad. Sci. USA. 99:11884-11889.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11884-11889
-
-
Chen, S.1
Ferrone, F.A.2
Wetzel, R.3
-
9
-
-
1442330474
-
From conversion to aggregation: Protofibril formation of the prion protein
-
DeMarco, M. L., and V. Daggett. 2004. From conversion to aggregation: protofibril formation of the prion protein. Proc. Natl. Acad. Sci. USA. 101:2293-2298.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2293-2298
-
-
Demarco, M.L.1
Daggett, V.2
-
10
-
-
0030579560
-
Prionics or the kinetic basis of prion diseases
-
Eigen, M. 1996. Prionics or the kinetic basis of prion diseases. Biophys. Chem. 63:A1-A18.
-
(1996)
Biophys. Chem.
, vol.63
-
-
Eigen, M.1
-
12
-
-
2942616602
-
Evidence for assembly of prions with left-handed β-helices into trimers
-
Govaerts, C., H. Wille, S. B. Prusiner, and F. E. Cohen. 2004. Evidence for assembly of prions with left-handed β-helices into trimers. Proc. Natl. Acad. Sci. USA. 101:8342-8347.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 8342-8347
-
-
Govaerts, C.1
Wille, H.2
Prusiner, S.B.3
Cohen, F.E.4
-
13
-
-
0035543109
-
The architecture of parallel β-helices and related folds
-
Jenkins, J., and R. Pickersgill. 2001. The architecture of parallel β-helices and related folds. Prog. Biophys. Mol. Biol. 77:111-175.
-
(2001)
Prog. Biophys. Mol. Biol.
, vol.77
, pp. 111-175
-
-
Jenkins, J.1
Pickersgill, R.2
-
14
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 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.W.4
Klein, M.L.5
-
15
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
Koradi, R., M. Billeter, and K. Wüthrich. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:51-55.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wüthrich, K.3
-
16
-
-
0035871686
-
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
-
Kräutler, V., W. F. van Gunsteren, and P. H. Hünenberger. 2001. A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. 22:501-508.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 501-508
-
-
Kräutler, V.1
Van Gunsteren, W.F.2
Hünenberger, P.H.3
-
17
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
18
-
-
0036784617
-
Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation
-
Ma, B., and R. Nussinov. 2002a. Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation. Protein Sci. 11:2335-2350.
-
(2002)
Protein Sci.
, vol.11
, pp. 2335-2350
-
-
Ma, B.1
Nussinov, R.2
-
20
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stole, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 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
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stole, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
21
-
-
0038455935
-
A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water
-
Mathias, G., B. Egwolf, M. Nonella, and P. Tavan. 2003. A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water. J. Chem. Phys. 118:10847-10860.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 10847-10860
-
-
Mathias, G.1
Egwolf, B.2
Nonella, M.3
Tavan, P.4
-
22
-
-
1842422953
-
Angular resolution and range of dipole-dipole correlations in water
-
Mathias, G., and P. Tavan. 2004. Angular resolution and range of dipole-dipole correlations in water. J. Chem. Phys. 120:4393-4403.
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 4393-4403
-
-
Mathias, G.1
Tavan, P.2
-
23
-
-
0000853232
-
A structure adapted multipole method or electrostatic interactions in protein dynamics
-
Niedermeier, C., and P. Tavan. 1994. A structure adapted multipole method or electrostatic interactions in protein dynamics. J. Chem. Phys. 101:734-748.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 734-748
-
-
Niedermeier, C.1
Tavan, P.2
-
24
-
-
0038717543
-
A prion protein epitope selective for the pathologically misfolded conformation
-
Paramithiotis, E., M. Pinard, T. Lawton, S. LaBoissiere, V. L. Leathers, W.-Q. Zou, L. A. Estey, J. Lamontagne, M. T. Lehto, L. H. Kondejewski, G. P. Francoeur, M. Papadopoulos, A. Haghighat, S. J. Spatz, M. Head, R. Will, J. Ironside, K. O'Rourke, Q. Tonelli, H. C. Ledebur, A. Chakrabartty, and N. R. Cashman. 2003. A prion protein epitope selective for the pathologically misfolded conformation. Nat. Med. 9:893-899.
-
(2003)
Nat. Med.
, vol.9
, pp. 893-899
-
-
Paramithiotis, E.1
Pinard, M.2
Lawton, T.3
Laboissiere, S.4
Leathers, V.L.5
Zou, W.-Q.6
Estey, L.A.7
Lamontagne, J.8
Lehto, M.T.9
Kondejewski, L.H.10
Francoeur, G.P.11
Papadopoulos, M.12
Haghighat, A.13
Spatz, S.J.14
Head, M.15
Will, R.16
Ironside, J.17
O'Rourke, K.18
Tonelli, Q.19
Ledebur, H.C.20
Chakrabartty, A.21
Cashman, N.R.22
more..
-
25
-
-
0037117519
-
Amyloid fibers are water-filled nanotubes
-
Perutz, M. F., J. T. Finch, J. Berriman, and A. Lesk. 2002a. Amyloid fibers are water-filled nanotubes. Proc. Natl. Acad. Sci. USA. 99:5591-5595.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5591-5595
-
-
Perutz, M.F.1
Finch, J.T.2
Berriman, J.3
Lesk, A.4
-
26
-
-
0037117499
-
Aggregation of proteins with expanded glutamine and alanine repeats of the glutamine-rich and asparagine-rich domains of Sup35 and of the amyloid β-peptide of amyloid plaques
-
Perutz, M. F., B. J. Pope, D. Owen, E. E. Wanker, and E. Scherzinger. 2002b. Aggregation of proteins with expanded glutamine and alanine repeats of the glutamine-rich and asparagine-rich domains of Sup35 and of the amyloid β-peptide of amyloid plaques. Proc. Natl. Acad. Sci. USA. 99:5596-5600.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5596-5600
-
-
Perutz, M.F.1
Pope, B.J.2
Owen, D.3
Wanker, E.E.4
Scherzinger, E.5
-
27
-
-
0037168655
-
A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR
-
Petkova, A. T., Y. Ishii, J. J. Balbach, O. N. Antzutkin, R. D. Leapman, F. Delaglio, and R. Tycko. 2002. A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl. Acad. Sci. USA. 99:16742-16747.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16742-16747
-
-
Petkova, A.T.1
Ishii, Y.2
Balbach, J.J.3
Antzutkin, O.N.4
Leapman, R.D.5
Delaglio, F.6
Tycko, R.7
-
28
-
-
0242443693
-
Force fields for protein simulation
-
Ponder, J. W., and D. A. Case. 2003. Force fields for protein simulation. Adv. Protein Chem. 66:27-85.
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
29
-
-
0028844306
-
A left-handed parallel β helix in the structure of UDP-N-acetylglucosamine acyltransferase
-
Raetz, C. R. H., and S. L. Roderick. 1995. A left-handed parallel β helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science. 270:997-1000.
-
(1995)
Science.
, vol.270
, pp. 997-1000
-
-
Raetz, C.R.H.1
Roderick, S.L.2
-
30
-
-
0037022563
-
Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
-
Richardson, J. S., and D. C. Richardson. 2002. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl. Acad. Sci. USA. 99:2754-2759.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 2754-2759
-
-
Richardson, J.S.1
Richardson, D.C.2
-
32
-
-
0037422616
-
Polyglutamine fibrillogenesis: The pathway unfolds
-
Ross, C. A., M. A. Poirier, E. E. Wanker, and M. Amzel. 2003. Polyglutamine fibrillogenesis: The pathway unfolds. Proc. Natl. Acad. Sci. USA. 100:1-3.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 1-3
-
-
Ross, C.A.1
Poirier, M.A.2
Wanker, E.E.3
Amzel, M.4
-
33
-
-
0033603336
-
Formation of fibrous aggregates from a non-native intermediate: Isolated P22 tailspike β-helix domain
-
Schuler, B., R. Rachel, and R. Seckler. 1999. Formation of fibrous aggregates from a non-native intermediate: isolated P22 tailspike β-helix domain. J. Biol. Chem. 274:18589-18596.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 18589-18596
-
-
Schuler, B.1
Rachel, R.2
Seckler, R.3
-
34
-
-
0031825554
-
From the globular to the fibrous state: Protein structure and structural conversion in amyloid formation
-
Sunde, M., and C. C. F. Blake. 1998. From the globular to the fibrous state: protein structure and structural conversion in amyloid formation. Q. Rev. Biophys. 31:1-39.
-
(1998)
Q. Rev. Biophys.
, vol.31
, pp. 1-39
-
-
Sunde, M.1
Blake, C.C.F.2
-
35
-
-
0031592945
-
Common core structure of amyloid fibrils by synchrotron X-ray diffraction
-
Sunde, M., L. C. Serpell, M. Bartlam, P. E. Fraser, M. B. Pepys, and C. C. F. Blake. 1997. Common core structure of amyloid fibrils by synchrotron X-ray diffraction. J. Mol. Biol. 273:729-739.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 729-739
-
-
Sunde, M.1
Serpell, L.C.2
Bartlam, M.3
Fraser, P.E.4
Pepys, M.B.5
Blake, C.C.F.6
-
36
-
-
84889839928
-
Molecular dynamics simulations of proteins and peptides: Problems, achievements, and perspectives
-
J. Buchner and T. Kiefhaber, editors. Wiley-VCH, Weinheim, Germany
-
Tavan, P., H. Carstens, and G. Mathias. 2005. Molecular dynamics simulations of proteins and peptides: problems, achievements, and perspectives. In Protein Folding Handbook, Part I. J. Buchner and T. Kiefhaber, editors. Wiley-VCH, Weinheim, Germany. 1170-1195.
-
(2005)
Protein Folding Handbook, Part I
, pp. 1170-1195
-
-
Tavan, P.1
Carstens, H.2
Mathias, G.3
-
37
-
-
0037168642
-
Mutational analysis of the structural organization of polyglutamine aggregates
-
Thakur, A., and R. Wetzel. 2002. Mutational analysis of the structural organization of polyglutamine aggregates. Proc. Natl. Acad. Sci. USA. 99:17014-17019.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 17014-17019
-
-
Thakur, A.1
Wetzel, R.2
-
38
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
-
van Gunsteren, W. F., and H. J. C. Berendsen. 1990. Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29:992-1023.
-
(1990)
Angew. Chem. Int. Ed. Engl.
, vol.29
, pp. 992-1023
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
39
-
-
0021476470
-
Calculations of electrostatic interactions in biological systems and in solutions
-
Warshel, A., and S. T. Russell. 1984. Calculations of electrostatic interactions in biological systems and in solutions. Q. Rev. Biophys. 17:283-422.
-
(1984)
Q. Rev. Biophys.
, vol.17
, pp. 283-422
-
-
Warshel, A.1
Russell, S.T.2
-
40
-
-
0037133587
-
Structural studies of the scrapie prion protein by electron crystallography
-
Wille, H., M. D. Michelitsch, V. Guénebaut, S. Supattapone, A. Serban. F. E. Cohen, D. A. Agard, and S. B. Prusiner. 2002. Structural studies of the scrapie prion protein by electron crystallography. Proc. Natl. Acad. Sci. USA. 99:3563-3568.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 3563-3568
-
-
Wille, H.1
Michelitsch, M.D.2
Guénebaut, V.3
Supattapone, S.4
Serban, A.5
Cohen, F.E.6
Agard, D.A.7
Prusiner, S.B.8
|