-
1
-
-
37149049312
-
X-ray solution scattering (SAXS) combined with crystallography and computation: Defining accurate macromolecular structures, conformations and assemblies in solution
-
C.D. Putnam, and M. Hammel J.A. Tainer X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Q. Rev. Biophys. 40 2007 191 285
-
(2007)
Q. Rev. Biophys.
, vol.40
, pp. 191-285
-
-
Putnam, C.D.1
Hammel, M.2
Tainer, J.A.3
-
2
-
-
0345169163
-
Small-angle scattering: A view on the properties, structures and structural changes of biological macromolecules in solution
-
M.H. Koch, P. Vachette, and D.I. Svergun Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution Q. Rev. Biophys. 36 2003 147 227
-
(2003)
Q. Rev. Biophys.
, vol.36
, pp. 147-227
-
-
Koch, M.H.1
Vachette, P.2
Svergun, D.I.3
-
3
-
-
84885861180
-
Impact and progress in small and wide angle x-ray scattering (SAXS and WAXS)
-
M.A. Graewert, and D.I. Svergun Impact and progress in small and wide angle x-ray scattering (SAXS and WAXS) Curr. Opin. Struct. Biol. 23 2013 748 754
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, pp. 748-754
-
-
Graewert, M.A.1
Svergun, D.I.2
-
4
-
-
52949104024
-
Characterization of protein fold by wide-angle x-ray solution scattering
-
L. Makowski, and D.J. Rodi R.F. Fischetti Characterization of protein fold by wide-angle x-ray solution scattering J. Mol. Biol. 383 2008 731 744
-
(2008)
J. Mol. Biol.
, vol.383
, pp. 731-744
-
-
Makowski, L.1
Rodi, D.J.2
Fischetti, R.F.3
-
5
-
-
5444263418
-
Wide-angle x-ray solution scattering as a probe of ligand-induced conformational changes in proteins
-
R.F. Fischetti, and D.J. Rodi L. Makowski Wide-angle x-ray solution scattering as a probe of ligand-induced conformational changes in proteins Chem. Biol. 11 2004 1431 1443
-
(2004)
Chem. Biol.
, vol.11
, pp. 1431-1443
-
-
Fischetti, R.F.1
Rodi, D.J.2
Makowski, L.3
-
6
-
-
33748488032
-
Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution x-ray scattering profiles
-
B. Zagrovic, and V.S. Pande Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution x-ray scattering profiles J. Am. Chem. Soc. 128 2006 11742 11743
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 11742-11743
-
-
Zagrovic, B.1
Pande, V.S.2
-
7
-
-
79955469012
-
WAXS studies of the structural diversity of hemoglobin in solution
-
L. Makowski, and J. Bardhan R.F. Fischetti WAXS studies of the structural diversity of hemoglobin in solution J. Mol. Biol. 408 2011 909 921
-
(2011)
J. Mol. Biol.
, vol.408
, pp. 909-921
-
-
Makowski, L.1
Bardhan, J.2
Fischetti, R.F.3
-
8
-
-
53249113119
-
Tracking the structural dynamics of proteins in solution using time-resolved wide-angle x-ray scattering
-
M. Cammarata, and M. Levantino H. Ihee Tracking the structural dynamics of proteins in solution using time-resolved wide-angle x-ray scattering Nat. Methods 5 2008 881 886
-
(2008)
Nat. Methods
, vol.5
, pp. 881-886
-
-
Cammarata, M.1
Levantino, M.2
Ihee, H.3
-
9
-
-
69849114705
-
Structural dynamics of light-driven proton pumps
-
M. Andersson, and E. Malmerberg R. Neutze Structural dynamics of light-driven proton pumps Structure 17 2009 1265 1275
-
(2009)
Structure
, vol.17
, pp. 1265-1275
-
-
Andersson, M.1
Malmerberg, E.2
Neutze, R.3
-
10
-
-
70349679105
-
Protein tertiary structural changes visualized by time-resolved x-ray solution scattering
-
S. Ahn, and K.H. Kim H. Ihee Protein tertiary structural changes visualized by time-resolved x-ray solution scattering J. Phys. Chem. B 113 2009 13131 13133
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 13131-13133
-
-
Ahn, S.1
Kim, K.H.2
Ihee, H.3
-
11
-
-
80053102933
-
Time-resolved WAXS reveals accelerated conformational changes in iodoretinal-substituted proteorhodopsin
-
E. Malmerberg, and Z. Omran R. Neutze Time-resolved WAXS reveals accelerated conformational changes in iodoretinal-substituted proteorhodopsin Biophys. J. 101 2011 1345 1353
-
(2011)
Biophys. J.
, vol.101
, pp. 1345-1353
-
-
Malmerberg, E.1
Omran, Z.2
Neutze, R.3
-
12
-
-
78649811402
-
Direct observation of myoglobin structural dynamics from 100 picoseconds to 1 microsecond with picosecond x-ray solution scattering
-
K.H. Kim, and K.Y. Oang H. Ihee Direct observation of myoglobin structural dynamics from 100 picoseconds to 1 microsecond with picosecond x-ray solution scattering Chem. Commun. (Camb.) 47 2011 289 291
-
(2011)
Chem. Commun. (Camb.)
, vol.47
, pp. 289-291
-
-
Kim, K.H.1
Oang, K.Y.2
Ihee, H.3
-
13
-
-
0037117502
-
Is the first hydration shell of lysozyme of higher density than bulk water?
-
F. Merzel, and J.C. Smith Is the first hydration shell of lysozyme of higher density than bulk water? Proc. Natl. Acad. Sci. USA 99 2002 5378 5383
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5378-5383
-
-
Merzel, F.1
Smith, J.C.2
-
14
-
-
0035965873
-
X-ray and neutron scattering analyses of hydration shells: A molecular interpretation based on sequence predictions and modelling fits
-
S.J. Perkins X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and modelling fits Biophys. Chem. 93 2001 129 139
-
(2001)
Biophys. Chem.
, vol.93
, pp. 129-139
-
-
Perkins, S.J.1
-
15
-
-
0029185933
-
CRYSOL - A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates
-
D. Svergun, C. Barberato, and M.H.J. Koch CRYSOL - a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Cryst. 28 1995 768 773
-
(1995)
J. Appl. Cryst.
, vol.28
, pp. 768-773
-
-
Svergun, D.1
Barberato, C.2
Koch, M.H.J.3
-
16
-
-
84863229972
-
Computation of small-angle scattering profiles with three-dimensional Zernike polynomials
-
H. Liu, and R.J. Morris P.H. Zwart Computation of small-angle scattering profiles with three-dimensional Zernike polynomials Acta Crystallogr. A 68 2012 278 285
-
(2012)
Acta Crystallogr. A
, vol.68
, pp. 278-285
-
-
Liu, H.1
Morris, R.J.2
Zwart, P.H.3
-
17
-
-
84882940564
-
Accurate SAXS profile computation and its assessment by contrast variation experiments
-
D. Schneidman-Duhovny, and M. Hammel A. Sali Accurate SAXS profile computation and its assessment by contrast variation experiments Biophys. J. 105 2013 962 974
-
(2013)
Biophys. J.
, vol.105
, pp. 962-974
-
-
Schneidman-Duhovny, D.1
Hammel, M.2
Sali, A.3
-
18
-
-
58749107160
-
Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics
-
C. Azuara, and H. Orland M. Delarue Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics Biophys. J. 95 2008 5587 5605
-
(2008)
Biophys. J.
, vol.95
, pp. 5587-5605
-
-
Azuara, C.1
Orland, H.2
Delarue, M.3
-
19
-
-
0000273258
-
An improved method for calculating the contribution of solvent to the x-ray diffraction pattern of biological molecules
-
R.D.B. Fraser, T.P. MacRae, and E. Suzuki An improved method for calculating the contribution of solvent to the x-ray diffraction pattern of biological molecules J. Appl. Cryst. 11 1978 693 694
-
(1978)
J. Appl. Cryst.
, vol.11
, pp. 693-694
-
-
Fraser, R.D.B.1
Macrae, T.P.2
Suzuki, E.3
-
20
-
-
78149240323
-
Improved fitting of solution x-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling
-
A. Grishaev, and L. Guo A. Bax Improved fitting of solution x-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling J. Am. Chem. Soc. 132 2010 15484 15486
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 15484-15486
-
-
Grishaev, A.1
Guo, L.2
Bax, A.3
-
21
-
-
70349331045
-
SoftWAXS: A computational tool for modeling wide-angle x-ray solution scattering from biomolecules
-
J. Bardhan, S. Park, and L. Makowski SoftWAXS: a computational tool for modeling wide-angle x-ray solution scattering from biomolecules J. Appl. Cryst. 42 2009 932 943
-
(2009)
J. Appl. Cryst.
, vol.42
, pp. 932-943
-
-
Bardhan, J.1
Park, S.2
Makowski, L.3
-
22
-
-
0036008508
-
SASSIM: A method for calculating small-angle x-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins
-
F. Merzel, and J.C. Smith SASSIM: a method for calculating small-angle x-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins Acta Crystallogr. D Biol. Crystallogr. 58 2002 242 249
-
(2002)
Acta Crystallogr. D Biol. Crystallogr.
, vol.58
, pp. 242-249
-
-
Merzel, F.1
Smith, J.C.2
-
23
-
-
67649373298
-
Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and x-ray scattering data analysis
-
T. Oroguchi, and H. Hashimoto M. Ikeguchi Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and x-ray scattering data analysis Biophys. J. 96 2009 2808 2822
-
(2009)
Biophys. J.
, vol.96
, pp. 2808-2822
-
-
Oroguchi, T.1
Hashimoto, H.2
Ikeguchi, M.3
-
24
-
-
64549083267
-
Simulated x-ray scattering of protein solutions using explicit-solvent models
-
S. Park, and J.P. Bardhan L. Makowski Simulated x-ray scattering of protein solutions using explicit-solvent models J. Chem. Phys. 130 2009 134114
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 134114
-
-
Park, S.1
Bardhan, J.P.2
Makowski, L.3
-
25
-
-
84878482877
-
Atomic-resolution structural information from scattering experiments on macromolecules in solution
-
J. Köfinger, and G. Hummer Atomic-resolution structural information from scattering experiments on macromolecules in solution Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 87 2013 052712
-
(2013)
Phys. Rev. e Stat. Nonlin. Soft Matter Phys.
, vol.87
, pp. 052712
-
-
Köfinger, J.1
Hummer, G.2
-
26
-
-
68949116065
-
A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes
-
S. Yang, and S. Park B. Roux A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes Biophys. J. 96 2009 4449 4463
-
(2009)
Biophys. J.
, vol.96
, pp. 4449-4463
-
-
Yang, S.1
Park, S.2
Roux, B.3
-
27
-
-
77957655386
-
Multidomain assembled states of Hck tyrosine kinase in solution
-
S. Yang, and L. Blachowicz B. Roux Multidomain assembled states of Hck tyrosine kinase in solution Proc. Natl. Acad. Sci. USA 107 2010 15757 15762
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 15757-15762
-
-
Yang, S.1
Blachowicz, L.2
Roux, B.3
-
28
-
-
78650948314
-
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions
-
B. Różycki, Y.C. Kim, and G. Hummer SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions Structure 19 2011 109 116
-
(2011)
Structure
, vol.19
, pp. 109-116
-
-
Rózycki, B.1
Kim, Y.C.2
Hummer, G.3
-
29
-
-
84980073071
-
X-ray scattering factors computed from numerical Hartree-Fock wave functions
-
D.T. Cromer, and J.B. Mann X-ray scattering factors computed from numerical Hartree-Fock wave functions Acta Crystallogr A24 1968 321 324
-
(1968)
Acta Crystallogr
, vol.24 A
, pp. 321-324
-
-
Cromer, D.T.1
Mann, J.B.2
-
30
-
-
84897441358
-
-
III ed. E. Prince, Springer Berlin, Heidelberg, Germany
-
P.J. Brown, and A.G. Fox B.T.M. Willis III ed. E. Prince, International Tables for Crystallography Vol. C 2006 Springer Berlin, Heidelberg, Germany 554 595
-
(2006)
International Tables for Crystallography
, vol.VOL. C
, pp. 554-595
-
-
Brown, P.J.1
Fox, A.G.2
Willis, B.T.M.3
-
31
-
-
0034316640
-
What can x-ray scattering tell us about the radial distribution functions of water?
-
J.M. Sorenson, and G. Hura T. Head-Gordon What can x-ray scattering tell us about the radial distribution functions of water? J. Chem. Phys. 113 2000 9149 9161
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 9149-9161
-
-
Sorenson, J.M.1
Hura, G.2
Head-Gordon, T.3
-
32
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Klein, M.L.3
-
33
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
B. Pullman, D. Reidel Dordrecht, The Netherlands
-
H.J.C. Berendsen, and J.P.M. Postma J. Hermans Interaction models for water in relation to protein hydration B. Pullman, Intermolecular Forces 1981 D. Reidel Dordrecht, The Netherlands 331 342
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Hermans, J.3
-
34
-
-
0000020246
-
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
-
M.W. Mahoney, and W.L. Jorgensen A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions J. Chem. Phys. 112 2000 8910 8922
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 8910-8922
-
-
Mahoney, M.W.1
Jorgensen, W.L.2
-
35
-
-
1942425662
-
A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums
-
S.W. Rick A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums J. Chem. Phys. 120 2004 6085 6093
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 6085-6093
-
-
Rick, S.W.1
-
36
-
-
78751525538
-
Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations
-
T. Oroguchi, and M. Ikeguchi Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations J. Chem. Phys. 134 2011 025102
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 025102
-
-
Oroguchi, T.1
Ikeguchi, M.2
-
37
-
-
84865406237
-
A hierarchical algorithm for fast Debye summation with applications to small angle scattering
-
N.A. Gumerov, and K. Berlin R. Duraiswami A hierarchical algorithm for fast Debye summation with applications to small angle scattering J. Comput. Chem. 33 2012 1981 1996
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 1981-1996
-
-
Gumerov, N.A.1
Berlin, K.2
Duraiswami, R.3
-
39
-
-
84875592758
-
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
-
S. Pronk, and S. Páll E. Lindahl GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 2013 845 854
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Páll, S.2
Lindahl, E.3
-
40
-
-
0000695363
-
High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission
-
M.C. Vaney, and S. Maignan A. Ducriux High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission Acta Crystallogr. D Biol. Crystallogr. 52 1996 505 517
-
(1996)
Acta Crystallogr. D Biol. Crystallogr.
, vol.52
, pp. 505-517
-
-
Vaney, M.C.1
Maignan, S.2
Ducriux, A.3
-
41
-
-
0032528033
-
Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
-
G. Cornilescu, and J.L. Marquardt A. Bax Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase J. Am. Chem. Soc. 120 1998 6836 6837
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 6836-6837
-
-
Cornilescu, G.1
Marquardt, J.L.2
Bax, A.3
-
42
-
-
0028080176
-
The third IgG-binding domain from streptococcal protein G. An analysis by x-ray crystallography of the structure alone and in a complex with Fab
-
J.P. Derrick, and D.B. Wigley The third IgG-binding domain from streptococcal protein G. An analysis by x-ray crystallography of the structure alone and in a complex with Fab J. Mol. Biol. 243 1994 906 918
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 906-918
-
-
Derrick, J.P.1
Wigley, D.B.2
-
43
-
-
0029645118
-
The low ionic strength crystal structure of horse cytochrome c at 2.1 A resolution and comparison with its high ionic strength counterpart
-
R. Sanishvili, and K.W. Volz E. Margoliash The low ionic strength crystal structure of horse cytochrome c at 2.1 A resolution and comparison with its high ionic strength counterpart Structure 3 1995 707 716
-
(1995)
Structure
, vol.3
, pp. 707-716
-
-
Sanishvili, R.1
Volz, K.W.2
Margoliash, E.3
-
44
-
-
84890168470
-
Energy barriers and driving forces in tRNA translocation through the ribosome
-
L.V. Bock, and C. Blau H. Grubmüller Energy barriers and driving forces in tRNA translocation through the ribosome Nat. Struct. Mol. Biol. 20 2013 1390 1396
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 1390-1396
-
-
Bock, L.V.1
Blau, C.2
Grubmüller, H.3
-
45
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
A.D. MacKerell, and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Karplus, M.3
-
46
-
-
79959720287
-
How robust are protein folding simulations with respect to force field parameterization?
-
S. Piana, K. Lindorff-Larsen, and D.E. Shaw How robust are protein folding simulations with respect to force field parameterization? Biophys. J. 100 2011 L47 L49
-
(2011)
Biophys. J.
, vol.100
-
-
Piana, S.1
Lindorff-Larsen, K.2
Shaw, D.E.3
-
47
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
A.D. Mackerell Jr., M. Feig, and C.L. Brooks III Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
48
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
V. Hornak, and R. Abel C. Simmerling Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 65 2006 712 725
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Simmerling, C.3
-
49
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Y. Duan, and C. Wu P. Kollman A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24 2003 1999 2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Kollman, P.3
-
50
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
51
-
-
2942622288
-
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
-
H.W. Horn, and W.C. Swope T. Head-Gordon Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew J. Chem. Phys. 120 2004 9665 9678
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 9665-9678
-
-
Horn, H.W.1
Swope, W.C.2
Head-Gordon, T.3
-
53
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
G. Bussi, D. Donadio, and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 2007 014101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
54
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
H.J.C. Berendsen, and J.P.M. Postma J.R. Haak 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
Haak, J.R.3
-
55
-
-
84986440341
-
Settle: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
S. Miyamoto, and P.A. Kollman Settle: An analytical version of the SHAKE and RATTLE algorithms for rigid water models J. Comput. Chem. 13 1992 952 962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
56
-
-
38749123962
-
P-LINCS: A parallel linear constraint solver for molecular simulation
-
B. Hess P-LINCS: A parallel linear constraint solver for molecular simulation J. Chem. Theory Comput. 4 2008 116 122
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
57
-
-
33846823909
-
Particle mesh Ewald: An N • log(N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an N • log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
59
-
-
84891946034
-
Mechanism of bacterial interference with TLR4 signaling by Brucella toll/interleukin-1 receptor domain-containing protein TcpB
-
M. Alaidarous, and T. Ve B. Kobe Mechanism of bacterial interference with TLR4 signaling by Brucella toll/interleukin-1 receptor domain-containing protein TcpB J. Biol. Chem. 289 2013 654 668
-
(2013)
J. Biol. Chem.
, vol.289
, pp. 654-668
-
-
Alaidarous, M.1
Ve, T.2
Kobe, B.3
-
60
-
-
78149463926
-
Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact
-
P. Florová, and P. Sklenovský M. Otyepka Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact J. Chem. Theory Comput. 6 2010 3569 3579
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3569-3579
-
-
Florová, P.1
Sklenovský, P.2
Otyepka, M.3
-
61
-
-
0037188386
-
Protein conformations explored by difference high-angle solution x-ray scattering: Oxidation state and temperature dependent changes in cytochrome C
-
D.M. Tiede, R. Zhang, and S. Seifert Protein conformations explored by difference high-angle solution x-ray scattering: oxidation state and temperature dependent changes in cytochrome C Biochemistry 41 2002 6605 6614
-
(2002)
Biochemistry
, vol.41
, pp. 6605-6614
-
-
Tiede, D.M.1
Zhang, R.2
Seifert, S.3
-
62
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
K. Lindorff-Larsen, and R.B. Best M. Vendruscolo Simultaneous determination of protein structure and dynamics Nature 433 2005 128 132
-
(2005)
Nature
, vol.433
, pp. 128-132
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Vendruscolo, M.3
-
63
-
-
0035079181
-
A refined solution structure of hen lysozyme determined using residual dipolar coupling data
-
H. Schwalbe, and S.B. Grimshaw L.J. Smith A refined solution structure of hen lysozyme determined using residual dipolar coupling data Protein Sci. 10 2001 677 688
-
(2001)
Protein Sci.
, vol.10
, pp. 677-688
-
-
Schwalbe, H.1
Grimshaw, S.B.2
Smith, L.J.3
-
64
-
-
67649494492
-
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
-
R.B. Best, and G. Hummer Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides J. Phys. Chem. B 113 2009 9004 9015
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
65
-
-
77955135754
-
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data
-
O.F. Lange, D. van der Spoel, and B.L. de Groot Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data Biophys. J. 99 2010 647 655
-
(2010)
Biophys. J.
, vol.99
, pp. 647-655
-
-
Lange, O.F.1
Van Der Spoel, D.2
De Groot, B.L.3
-
66
-
-
84857463877
-
Systematic validation of protein force fields against experimental data
-
K. Lindorff-Larsen, and P. Maragakis D.E. Shaw Systematic validation of protein force fields against experimental data PLoS ONE 7 2012 e32131
-
(2012)
PLoS ONE
, vol.7
, pp. 32131
-
-
Lindorff-Larsen, K.1
Maragakis, P.2
Shaw, D.E.3
-
67
-
-
84958060673
-
Fast and robust smallest enclosing balls
-
Springer Berlin, Heidelberg, Germany
-
B. Gärtner Fast and robust smallest enclosing balls Algorithms-ESA99 1999 Springer Berlin, Heidelberg, Germany 325 338
-
(1999)
Algorithms-ESA99
, pp. 325-338
-
-
Gärtner, B.1
|