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Molecular-dynamics simulations of biological macromolecules
International Tables for Crystallography (2012). Vol. F, ch. 20.2, pp. 642-648 [ doi:10.1107/97809553602060000878 ]
... of an enzyme complex was of hen egg-white lysozyme (Post et al., 1986), the first enzyme whose structure was solved ... are force constants, and are equilibrium values for bond lengths, b, and angles, [theta], respectively, and [varphi] is the torsion angle ... high frequency, small amplitude motions (i.e. those modelled by crystallographic B values) to low frequency, larger amplitude motions of loops ...
Assessment of the simulation procedure
International Tables for Crystallography (2012). Vol. F, Section 20.2.7, p. 645 [ doi:10.1107/97809553602060000878 ]
... a time series can be used to detect conformational transitions (Post et al., 1989). Figure 20.2.7.1 | | Structural comparison and radii ... Left: r.m.s. coordinate differences averaged over main-chain atoms (N, C[alpha], C) between the energy-minimized crystallographic structure and the simulation ...
Internal dynamics and average structures
International Tables for Crystallography (2012). Vol. F, Section 20.2.6, pp. 644-645 [ doi:10.1107/97809553602060000878 ]
... high frequency, small amplitude motions (i.e. those modelled by crystallographic B values) to low frequency, larger amplitude motions of loops and whole domains. Some studies (Kuriyan et al., 1986; Post, 1992) have examined the validity of the assumptions about fast ... evaluation by molecular dynamics. J. Mol. Biol. 190, 455-479. Post, C. B. (1992). Internal motional averaging and three- ...
Modifications in the force field for structure determination
International Tables for Crystallography (2012). Vol. F, Section 20.2.5, p. 644 [ doi:10.1107/97809553602060000878 ]
Modifications in the force field for structure determination 20.2.5. Modifications in the force field for structure determination Simulated-annealing protocols require modification of the parameters to maintain the correct geometry and local structural integrity of the molecule in order to allow heating to very high, non-physical temperatures for several thousand ...
Empirical parameterization of the force field
International Tables for Crystallography (2012). Vol. F, Section 20.2.4, p. 644 [ doi:10.1107/97809553602060000878 ]
... D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E. III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J. & ...
Experimental restraints in the energy function
International Tables for Crystallography (2012). Vol. F, Section 20.2.3.3, pp. 643-644 [ doi:10.1107/97809553602060000878 ]
Experimental restraints in the energy function 20.2.3.3. Experimental restraints in the energy function For the purpose of structure determination, the potential-energy function used for molecular-dynamics calculation incorporates the information from experimental data in the form of non-physical restraint terms. These restraint terms, introduced to bias the conformational sampling ...
[more results from section 20.2.3 in volume F]
The simulation method
International Tables for Crystallography (2012). Vol. F, Section 20.2.2, p. 642 [ doi:10.1107/97809553602060000878 ]
... 1967) or a variation, Leapfrog, is commonly used. References Brooks, C. L. III, Karplus, M. & Pettitt, B. M. (1988). Proteins: a theoretical perspective of dynamics, structure ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 20.2.1, p. 642 [ doi:10.1107/97809553602060000878 ]
... of an enzyme complex was of hen egg-white lysozyme (Post et al., 1986), the first enzyme whose structure was solved ... D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E. III, Roux, B., Schlenkrich, M., Smith, ...
Effect of crystallographic atomic resolution on structural stability during molecular dynamics
International Tables for Crystallography (2012). Vol. F, Section 20.2.8, pp. 645-647 [ doi:10.1107/97809553602060000878 ]
... 2.15 2.05 1.9 2.17 2.13 1.85 2.17 2.15 Figure 20.2.8.1 | | C[alpha] tracings of BPTI. Left: crystallographic structures determined from data ... The r.m.s.d. is averaged over the main-chain atoms N, C[alpha] and C. References Caves, L. S. D., Evanseck, J. D. & Karplus, ...
International Tables for Crystallography (2012). Vol. F, ch. 20.2, pp. 642-648 [ doi:10.1107/97809553602060000878 ]
... of an enzyme complex was of hen egg-white lysozyme (Post et al., 1986), the first enzyme whose structure was solved ... are force constants, and are equilibrium values for bond lengths, b, and angles, [theta], respectively, and [varphi] is the torsion angle ... high frequency, small amplitude motions (i.e. those modelled by crystallographic B values) to low frequency, larger amplitude motions of loops ...
Assessment of the simulation procedure
International Tables for Crystallography (2012). Vol. F, Section 20.2.7, p. 645 [ doi:10.1107/97809553602060000878 ]
... a time series can be used to detect conformational transitions (Post et al., 1989). Figure 20.2.7.1 | | Structural comparison and radii ... Left: r.m.s. coordinate differences averaged over main-chain atoms (N, C[alpha], C) between the energy-minimized crystallographic structure and the simulation ...
Internal dynamics and average structures
International Tables for Crystallography (2012). Vol. F, Section 20.2.6, pp. 644-645 [ doi:10.1107/97809553602060000878 ]
... high frequency, small amplitude motions (i.e. those modelled by crystallographic B values) to low frequency, larger amplitude motions of loops and whole domains. Some studies (Kuriyan et al., 1986; Post, 1992) have examined the validity of the assumptions about fast ... evaluation by molecular dynamics. J. Mol. Biol. 190, 455-479. Post, C. B. (1992). Internal motional averaging and three- ...
Modifications in the force field for structure determination
International Tables for Crystallography (2012). Vol. F, Section 20.2.5, p. 644 [ doi:10.1107/97809553602060000878 ]
Modifications in the force field for structure determination 20.2.5. Modifications in the force field for structure determination Simulated-annealing protocols require modification of the parameters to maintain the correct geometry and local structural integrity of the molecule in order to allow heating to very high, non-physical temperatures for several thousand ...
Empirical parameterization of the force field
International Tables for Crystallography (2012). Vol. F, Section 20.2.4, p. 644 [ doi:10.1107/97809553602060000878 ]
... D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E. III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J. & ...
Experimental restraints in the energy function
International Tables for Crystallography (2012). Vol. F, Section 20.2.3.3, pp. 643-644 [ doi:10.1107/97809553602060000878 ]
Experimental restraints in the energy function 20.2.3.3. Experimental restraints in the energy function For the purpose of structure determination, the potential-energy function used for molecular-dynamics calculation incorporates the information from experimental data in the form of non-physical restraint terms. These restraint terms, introduced to bias the conformational sampling ...
[more results from section 20.2.3 in volume F]
The simulation method
International Tables for Crystallography (2012). Vol. F, Section 20.2.2, p. 642 [ doi:10.1107/97809553602060000878 ]
... 1967) or a variation, Leapfrog, is commonly used. References Brooks, C. L. III, Karplus, M. & Pettitt, B. M. (1988). Proteins: a theoretical perspective of dynamics, structure ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 20.2.1, p. 642 [ doi:10.1107/97809553602060000878 ]
... of an enzyme complex was of hen egg-white lysozyme (Post et al., 1986), the first enzyme whose structure was solved ... D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E. III, Roux, B., Schlenkrich, M., Smith, ...
Effect of crystallographic atomic resolution on structural stability during molecular dynamics
International Tables for Crystallography (2012). Vol. F, Section 20.2.8, pp. 645-647 [ doi:10.1107/97809553602060000878 ]
... 2.15 2.05 1.9 2.17 2.13 1.85 2.17 2.15 Figure 20.2.8.1 | | C[alpha] tracings of BPTI. Left: crystallographic structures determined from data ... The r.m.s.d. is averaged over the main-chain atoms N, C[alpha] and C. References Caves, L. S. D., Evanseck, J. D. & Karplus, ...
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