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Molecular-dynamics simulations of biological macromolecules
Post, C. B. and Dadarlat, V. M.  International Tables for Crystallography (2012). Vol. F, ch. 20.2, pp. 642-648 [ doi:10.1107/97809553602060000878 ]
... zero as increases. The term is the reciprocal Ewald sum: V is the volume and m is a vector in the reciprocal space. The Ewald sum ... Mol. Biol. 249, 604-624. Brooks, C. L. III, Karplus, M. & Pettitt, B. M. (1988). Proteins: a theoretical perspective ...

Assessment of the simulation procedure
Post, C. B. and Dadarlat, V. M.  International Tables for Crystallography (2012). Vol. F, Section 20.2.7, p. 645 [ doi:10.1107/97809553602060000878 ]
... Chem. Phys. 98, 10089-10092. Essmann, U., Perrera, L., Berkovitz, M. L., Darden, T., Lee, H. & Pedersen, L. G. (1995). ... space distributions. Phys. Rev. A, 31, 1695-1697. Levy, R. M., Karplus, M. & McCammon, J. A. (1981). Increase of 13C NMR ...

Internal dynamics and average structures
Post, C. B. and Dadarlat, V. M.  International Tables for Crystallography (2012). Vol. F, Section 20.2.6, pp. 644-645 [ doi:10.1107/97809553602060000878 ]
... 1995). References Kuriyan, J., Petsko, G. A., Levy, R. M. & Karplus, M. (1986). Effect of anisotropy and anharmonicity on protein crystallographic ...

Modifications in the force field for structure determination
Post, C. B. and Dadarlat, V. M.  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
Post, C. B. and Dadarlat, V. M.  International Tables for Crystallography (2012). Vol. F, Section 20.2.4, p. 644 [ doi:10.1107/97809553602060000878 ]
... L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983). Comparison of simple potential functions for simulating ... Soc. 110, 1657-1666. MacKerell, A., Wiorkiewicz-Kuczera, J. & Karplus, M. (1995). An all atom empirical energy function for the ... 117, 11946-11975. MacKerell, A. D. Jr, Bashford, D., Bellott, M., Dunbrack, R. L. Jr, Evanseck, J. D., Field, M. ...

Experimental restraints in the energy function
Post, C. B. and Dadarlat, V. M.  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
Post, C. B. and Dadarlat, V. M.  International Tables for Crystallography (2012). Vol. F, Section 20.2.2, p. 642 [ doi:10.1107/97809553602060000878 ]
... Leapfrog, is commonly used. References Brooks, C. L. III, Karplus, M. & Pettitt, B. M. (1988). Proteins: a theoretical perspective of dynamics, structure and thermodynamics. Adv. Chem. Phys. 71, 1-259. Goodfellow, J. M. & Levy, R. M. (1998). Theory and simulation. Curr. ...

Introduction
Post, C. B. and Dadarlat, V. M.  International Tables for Crystallography (2012). Vol. F, Section 20.2.1, p. 642 [ doi:10.1107/97809553602060000878 ]
... 1987). References Brünger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science ... 282, 740-744. MacKerell, A. D. Jr, Bashford, D., Bellott, M., Dunbrack, R. L. Jr, Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., ...

Effect of crystallographic atomic resolution on structural stability during molecular dynamics
Post, C. B. and Dadarlat, V. M.  International Tables for Crystallography (2012). Vol. F, Section 20.2.8, pp. 645-647 [ doi:10.1107/97809553602060000878 ]
... C. References Caves, L. S. D., Evanseck, J. D. & Karplus, M. (1998). Locally accessible conformations of proteins: multiple molecular dynamics ... 92, 2740-2741. Hamiaux, C., Prangé, T., Ričs-Kautt, M., Ducruix, A., Lafont, S., Astier, J. P. & Veesler, S. (1999 ...

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