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Submission Details

Submission Title

MDFF in vacuo, solvent and membrane

Submission Authors

  • Kwok-Yan Chan
  • Leonardo G. Trabuco
  • Eduard Schreiner
  • Klaus Schulten

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Submission Comments

The provided structure (pdb 3M9I) was fitted into the provided map by the molecular dynamics flexible fitting (MDFF) method. MDFF is a MD based fitting method and so the system can be prepared in different environment to perform the fitting. Here, the fittings were done in vacuo, in solvent and in membrane.

Chiral errors and cis-peptide bonds in the starting structure were corrected by 2 VMD plugins, Chirality and Cispeptide, and restraints were used to prevent such errors during the fitting.

3M9I-vacuo.pdb - Fitting in vacuo

3M9I-solvent.pdb - Fitting in solvent, here we first let the water and ions equilibrate by constraining the protein, and next we let the side chains equilibrate as well and finally performed the fitting.

3M9I-membrane.pdb - Fitting in membrane, here we first let the water, ions and membrane equilibrate by constraining the protein, and next we let the side chains equilibrate as well and finally performed the fitting.

As a comparison, we fit another structure (pdb 2B6O, with both terminus cut to have same sequence as the given pdb 3M9I) into the map as well.

2B6O-vacuo.pdb - Fitting in vacuo

2B6O-solvent.pdb - Fitting in solvent, here we first let the water and ions equilibrate by constraining the protein, and next we let the side chains equilibrate as well and finally performed the fitting.

2B6O-membrane.pdb - Fitting in membrane, here we first let the water, ions and membrane equilibrate by constraining the protein, and next we let the side chains equilibrate as well and finally performed the fitting.

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Submitted PDB Models:

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