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How can high-resolution structural information be imposed on a lower-resolution full protein model in simulations?

a. Use Real Space Refine program in PHENIX.
b. Utilize the Flexible Fitting plugin in VMD.
c. Apply Chimera's rigid body fitting.
d. All of the above.

1 Answer

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Final answer:

High-resolution structural information can be integrated into low-resolution protein models using the Real Space Refine program in PHENIX, the Flexible Fitting plugin in VMD, and Chimera's rigid body fitting, either individually or in combination.

Step-by-step explanation:

High-resolution structural information can be combined with a lower-resolution full protein model in simulations through various methods. Real Space Refine program in PHENIX allows for the refinement of macromolecule structures based on high-resolution data. The Flexible Fitting plugin in VMD facilitates the fitting of atomic structures into density maps, which is useful when integrating high-resolution local structures into a global low-resolution model. Additionally, Chimera's rigid body fitting technique provides a way to fit high-resolution structures into low-resolution maps. All these tools can be utilized independently or in combination, depending on the requirements of the protein modeling task.

In simulations, high-resolution structural information can be imposed on a lower-resolution full protein model using various methods. One approach is to use the Real Space Refine program in PHENIX, which iteratively adjusts the low-resolution model to match the high-resolution data. Another option is to utilize the Flexible Fitting plugin in VMD, which allows for flexible adjustments of the atomic positions in the model to fit the high-resolution data. Chimera's rigid body fitting is another method that can be applied, which aligns a known high-resolution structure with multiple conformations of the low-resolution model.

User Han Zhao
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