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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

Fitted a homology model (based on the closed state structure) into the map provided (which is in open state) 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. Symmetry restraints were used to maintain the symmetry.

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.

open-fitted.pdb - Fitting without symmetry restraints

open-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

Fitted a homology model (based on the closed state structure) into the map provided (which is in open state) 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. Symmetry restraints were used to maintain the symmetry.

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.

open-fitted.pdb - Fitting without symmetry restraints

open-symmetry.pdb - Fitting with symmetry restraints

Files

Submitted Maps:

Submitted PDB Models:

Other files:



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