-
1
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M., and J. A. McCammon. 2002. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:646-652.
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
2
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
Adcock, S. A., and J. A. McCammon. 2006. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev. 106:1589-1615.
-
(2006)
Chem. Rev
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
3
-
-
17044393884
-
Coarse-grained models of proteins
-
Tozzini, V. 2005. Coarse-grained models of proteins. Curr. Opin. Struct. Biol. 15:144-150.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
4
-
-
34247098754
-
Multiscale modeling of biomolecular systems: In serial and in parallel
-
Ayton, G. S., W. G. Noid, and G. A. Voth. 2007. Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol. 17:192-198.
-
(2007)
Curr. Opin. Struct. Biol
, vol.17
, pp. 192-198
-
-
Ayton, G.S.1
Noid, W.G.2
Voth, G.A.3
-
5
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
Izvekov, S., and G. A. Voth. 2005. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B. 109:2469-2473.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
6
-
-
34247852583
-
Coarse-grained peptide modeling using a systematic multiscale approach
-
Zhou, J., I. F. Thorpe, S. Izvekov, and G. A. Voth. 2007. Coarse-grained peptide modeling using a systematic multiscale approach. Biophys. J. 92:4289-4303.
-
(2007)
Biophys. J
, vol.92
, pp. 4289-4303
-
-
Zhou, J.1
Thorpe, I.F.2
Izvekov, S.3
Voth, G.A.4
-
7
-
-
33748266722
-
Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
-
Shi, Q., S. Izvekov, and G. A. Voth. 2006. Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. J. Phys. Chem. B. 110:15045-15048.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 15045-15048
-
-
Shi, Q.1
Izvekov, S.2
Voth, G.A.3
-
8
-
-
34548835493
-
Coarse-grained representation of β-helical protein building blocks
-
Curcó, D., R. Nussinov, and C. Alemán. 2007. Coarse-grained representation of β-helical protein building blocks. J. Phys. Chem. B. 111:10538-10549.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 10538-10549
-
-
Curcó, D.1
Nussinov, R.2
Alemán, C.3
-
9
-
-
34147113306
-
Use of constrained synthetic amino acids in β-helix proteins for conformational control
-
Zanuy, D., A. I. Jiménez, C. Cativiela, R. Nussinov, and C. Alemán. 2007. Use of constrained synthetic amino acids in β-helix proteins for conformational control. J. Phys. Chem. B. 111:3236-3242.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 3236-3242
-
-
Zanuy, D.1
Jiménez, A.I.2
Cativiela, C.3
Nussinov, R.4
Alemán, C.5
-
10
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter atomic analysis
-
Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys. Rev. Lett. 77:1905-1908.
-
(1996)
Phys. Rev. Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
11
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
-
(2001)
Biophys. J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
12
-
-
0034699383
-
Image reconstructions of helical assemblies of the HIV-1 CA protein
-
Li, S., C. P. Hill, W. I. Sundquist, and J. T. Finch. 2000. Image reconstructions of helical assemblies of the HIV-1 CA protein. Nature. 407:409-413.
-
(2000)
Nature
, vol.407
, pp. 409-413
-
-
Li, S.1
Hill, C.P.2
Sundquist, W.I.3
Finch, J.T.4
-
13
-
-
24944541377
-
Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis
-
Chu, J. W., and G. A. Voth. 2005. Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc. Natl. Acad. Sci. USA. 102:13111-13116.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13111-13116
-
-
Chu, J.W.1
Voth, G.A.2
-
14
-
-
33646123091
-
Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
-
Chu, J. W., and G. A. Voth. 2006. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J. 90:1572-1582.
-
(2006)
Biophys. J
, vol.90
, pp. 1572-1582
-
-
Chu, J.W.1
Voth, G.A.2
-
15
-
-
33748448490
-
A natural coarse-graining for simulating large biomolecular motion
-
Gohlke, H., and M. F. Thorpe. 2006. A natural coarse-graining for simulating large biomolecular motion. Biophys. J. 91:2115-2120.
-
(2006)
Biophys. J
, vol.91
, pp. 2115-2120
-
-
Gohlke, H.1
Thorpe, M.F.2
-
16
-
-
0000785338
-
Generic rigidity percolation: The pebble game
-
Jacobs, D. J., and M. F. Thorpe. 1995. Generic rigidity percolation: the pebble game. Phys. Rev. Lett. 75:4051-4054.
-
(1995)
Phys. Rev. Lett
, vol.75
, pp. 4051-4054
-
-
Jacobs, D.J.1
Thorpe, M.F.2
-
17
-
-
0028204732
-
Topology representing networks
-
Martinez, T., and K. Schulten. 1994. Topology representing networks. Neural Netw. 7:507-522.
-
(1994)
Neural Netw
, vol.7
, pp. 507-522
-
-
Martinez, T.1
Schulten, K.2
-
18
-
-
33845204189
-
Stability and dynamics of virus capsids described by coarse-grained modeling
-
Arkhipov, A., P. L. Freddolino, and K. Schulten. 2006. Stability and dynamics of virus capsids described by coarse-grained modeling. Structure. 14:1767-1777.
-
(2006)
Structure
, vol.14
, pp. 1767-1777
-
-
Arkhipov, A.1
Freddolino, P.L.2
Schulten, K.3
-
19
-
-
43049125805
-
Spectral coarse-graining and synchronization in oscillator networks
-
Gfeller, D., and P. De Los Rios. 2008. Spectral coarse-graining and synchronization in oscillator networks. Phys. Rev. Lett. 100:174104.
-
(2008)
Phys. Rev. Lett
, vol.100
, pp. 174104
-
-
Gfeller, D.1
De Los Rios, P.2
-
21
-
-
0033117937
-
Investigating protein dynamics in collective coordinate space
-
Kitao, A., and N. Go. 1999. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. 9:164-169.
-
(1999)
Curr. Opin. Struct. Biol
, vol.9
, pp. 164-169
-
-
Kitao, A.1
Go, N.2
-
22
-
-
0034127361
-
Collective protein dynamics in relation to function
-
Berendsen, H. J. C., and S. Hayward. 2000. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. 10:165-169.
-
(2000)
Curr. Opin. Struct. Biol
, vol.10
, pp. 165-169
-
-
Berendsen, H.J.C.1
Hayward, S.2
-
23
-
-
36749036031
-
Dynamics of essential collective motions in proteins: Theory
-
Stepanova, M. 2007. Dynamics of essential collective motions in proteins: theory. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 76:051918.
-
(2007)
Phys. Rev. E Stat. Nonlin. Soft Matter Phys
, vol.76
, pp. 051918
-
-
Stepanova, M.1
-
24
-
-
0030888546
-
Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
-
Hayward, S., and H. J. C. Berendsen. 1997. Model-free methods of analyzing domain motions in proteins from simulations: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins Struct. Funct. Genet. 27:425-437.
-
(1997)
Proteins Struct. Funct. Genet
, vol.27
, pp. 425-437
-
-
Hayward, S.1
Berendsen, H.J.C.2
-
25
-
-
33745714391
-
Dynamic protein domains: Identification, interdependence, and stability
-
Yesylevskyy, S. O., V. N. Kharkyanen, and A. P. Demchenko. 2006. Dynamic protein domains: identification, interdependence, and stability. Biophys. J. 91:670-685.
-
(2006)
Biophys. J
, vol.91
, pp. 670-685
-
-
Yesylevskyy, S.O.1
Kharkyanen, V.N.2
Demchenko, A.P.3
-
27
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
-
(1953)
J. Chem. Phys
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
28
-
-
0032925240
-
Structures of the HIV-1 capsid protein dimerization domain at 2.6 Å resolution
-
Worthylake, D. K., H. Wang, S. Yoo, W. I. Sundquist, and C. P. Hill. 1999. Structures of the HIV-1 capsid protein dimerization domain at 2.6 Å resolution. Acta Crystallogr. D Biol. Crystallogr. 55:85-92.
-
(1999)
Acta Crystallogr. D Biol. Crystallogr
, vol.55
, pp. 85-92
-
-
Worthylake, D.K.1
Wang, H.2
Yoo, S.3
Sundquist, W.I.4
Hill, C.P.5
-
29
-
-
0038780573
-
Structural insights into the catalytic mechanism of cyclophilin A
-
Howard, B. R., F. F. Vajdos, S. Li, W. I. Sundquist, and C. P. Hill. 2003. Structural insights into the catalytic mechanism of cyclophilin A. Nat. Struct. Biol. 10:475-481.
-
(2003)
Nat. Struct. Biol
, vol.10
, pp. 475-481
-
-
Howard, B.R.1
Vajdos, F.F.2
Li, S.3
Sundquist, W.I.4
Hill, C.P.5
-
30
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B., R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
31
-
-
85031362593
-
-
Grubmüller, H. 1996. SOLVATE v. 1.0. Theoretical Biophysics Group, Institute for Medical Optics, Ludwig-Maximilians University, Munich.
-
Grubmüller, H. 1996. SOLVATE v. 1.0. Theoretical Biophysics Group, Institute for Medical Optics, Ludwig-Maximilians University, Munich.
-
-
-
-
32
-
-
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
-
33
-
-
33846823909
-
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
-
Darden, T., D. York, and L. Pedersen. 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
-
34
-
-
8344276781
-
NAMD - A parallel, object-oriented molecular dynamics program
-
Nelson, M., W. Humphrey, A. Gursoy, A. Dalke, L. Kalé, R. D. Skeel, and K. Schulten. 1996. NAMD - A parallel, object-oriented molecular dynamics program. J. Supercomput. App. 10:251-268.
-
(1996)
J. Supercomput. App
, vol.10
, pp. 251-268
-
-
Nelson, M.1
Humphrey, W.2
Gursoy, A.3
Dalke, A.4
Kalé, L.5
Skeel, R.D.6
Schulten, K.7
-
35
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten. 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
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
36
-
-
36449003554
-
Constant pressure molecular dynamics algorithms
-
Martyna, G. J., D. J. Tobias, and M. L. Klein. 1994. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101:4177-4189.
-
(1994)
J. Chem. Phys
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
37
-
-
36449007836
-
Constant pressure molecular dynamics simulation - the Langevin piston method
-
Feller, S. E., Y. H. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation - the Langevin piston method. J. Chem. Phys. 103:4613-4621.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
38
-
-
0141445972
-
Crystal structure of monomeric actin in the ATP state. structural basis of nucleotide-dependent actin dynamics
-
Graceffa, P., and R. Dominguez. 2003. Crystal structure of monomeric actin in the ATP state. structural basis of nucleotide-dependent actin dynamics. J. Biol. Chem. 278:34172-34180.
-
(2003)
J. Biol. Chem
, vol.278
, pp. 34172-34180
-
-
Graceffa, P.1
Dominguez, R.2
-
39
-
-
0041784950
-
-
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. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-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.
-
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. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-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.
-
-
-
-
40
-
-
0024988340
-
Atomic structure of the actin: DNase I complex
-
Kabsch, W., H. G. Mannherz, D. Suck, E. F. Pai, and K. C. Holmes. 1990. Atomic structure of the actin: DNase I complex. Nature. 347:37-44.
-
(1990)
Nature
, vol.347
, pp. 37-44
-
-
Kabsch, W.1
Mannherz, H.G.2
Suck, D.3
Pai, E.F.4
Holmes, K.C.5
-
42
-
-
0027134594
-
The actin/actin interactions involving the N-terminus of the DNAse-I-binding loop are crucial for stabilization of the actin filament
-
Khaitlina, S. Y., J. Moraczewska, and H. Strzeleckagolaszewska. 1993. The actin/actin interactions involving the N-terminus of the DNAse-I-binding loop are crucial for stabilization of the actin filament. Eur. J. Biochem. 218:911-920.
-
(1993)
Eur. J. Biochem
, vol.218
, pp. 911-920
-
-
Khaitlina, S.Y.1
Moraczewska, J.2
Strzeleckagolaszewska, H.3
-
43
-
-
34548226450
-
Nucleotide effects on the structure and dynamics of actin
-
Zheng, X., K. Diraviyam, and D. Sept. 2007. Nucleotide effects on the structure and dynamics of actin. Biophys. J. 93:1277-1283.
-
(2007)
Biophys. J
, vol.93
, pp. 1277-1283
-
-
Zheng, X.1
Diraviyam, K.2
Sept, D.3
-
44
-
-
33845381177
-
Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
-
Arkhipov, A., P. L. Freddolino, K. Imada, K. Namba, and K. Schulten. 2006. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophys. J. 91:4589-4597.
-
(2006)
Biophys. J
, vol.91
, pp. 4589-4597
-
-
Arkhipov, A.1
Freddolino, P.L.2
Imada, K.3
Namba, K.4
Schulten, K.5
-
45
-
-
53249125167
-
-
Arkhipov, A., Y. Yin, and K. Schulten. 2008. Four-scale description of membrane sculpting by BAR domains. Biophys. J. Published on Biophysical Journal BioFast, on May 30, 2008.
-
Arkhipov, A., Y. Yin, and K. Schulten. 2008. Four-scale description of membrane sculpting by BAR domains. Biophys. J. Published on Biophysical Journal BioFast, on May 30, 2008.
-
-
-
-
46
-
-
1842850600
-
Voronoi and Voronoi-related tessellations in studies of protein structure and interaction
-
Poupon, A. 2004. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr. Opin. Struct. Biol. 14:233-241.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 233-241
-
-
Poupon, A.1
-
47
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
Balsera, M. A., W. Wriggers, Y. Oono, and K. Schulten. 1996. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100:2567-2572.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 2567-2572
-
-
Balsera, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
48
-
-
0032802062
-
On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
-
Amadei, A., M. A. Ceruso, and A. Di Nola. 1999. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins Struct. Funct. Genet. 36:419-424.
-
(1999)
Proteins Struct. Funct. Genet
, vol.36
, pp. 419-424
-
-
Amadei, A.1
Ceruso, M.A.2
Di Nola, A.3
|