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Submission Details

Submission Title

MDFF with symmetry restraints

Submission Authors

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

(hint: click '+' to add more items)

Submission Comments

The provided structure (pdb 3LOS) was fitted into the provided map by the molecular dynamics flexible fitting method. Fittings were done in solvent and 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.

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.

Restraints to maintain the symmetry of the system were used and results of fitting with and without symmetry restraints can be compared.

3LOS-fitted.pdb - Fitting without symmetry restraints

3LOS-symmetry.pdb - Fitting with symmetry restraints

Files

Submitted Maps:

Submitted PDB Models:

Other files:



Images and screenshots


Representative Image:

Screenshots and other example images:

Submission Details

Submission Title

MDFF with symmetry restraints

Submission Authors

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

(hint: click '+' to add more items)

Submission Comments

The provided structure (pdb 3LOS) was fitted into the provided map by the molecular dynamics flexible fitting method. Fittings were done in solvent and 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.

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.

Restraints to maintain the symmetry of the system were used and results of fitting with and without symmetry restraints can be compared.

3LOS-fitted.pdb - Fitting without symmetry restraints

3LOS-symmetry.pdb - Fitting with symmetry restraints

Files

Submitted Maps:

Submitted PDB Models:

Other files:



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