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Representative Image: 2C7DU_model_vs_native_v1.png

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Submission Details

Submission Title

model for 2C7DU

Submission Authors

  • Steffen Lindert
  • Tommy Hofmann
  • Nils Woetzel
  • Jens Meiler

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

Submission Comments

We developed an algorithm, EM-Fold, that predicts secondary structure elements from the primary sequence of the protein and folds these into identified regions corresponding to secondary structure in the density map. So for the purpose of this challenge we assumed that the provided density maps had been segmented into small density maps that only contain the individual chains of the proteins. We then identify positions of secondary structure elements in the map. Then EM-Fold (S. Lindert et al., Structure 17, 990 (Jul 15, 2009)) was used to assemble predicted SSEs into these density rods and refine positions of SSEs in these density rods. Finally Rosetta (F. DiMaio et al., J Mol Biol 392, 181 (Sep 11, 2009)) was used to build loops and side chains as well as refine further the best scoring models from EM-Fold. For this a three step protocol was used that identified the regions that agree least with density and then rebuilds coordinated for these. Due to time constraints for the submission of initial results we already submitted the Rosetta models after the first of the three iterative steps of refinement. We report rmsds of our models to the native chain (over full lenght protein and over the helical residues only).

We worked on map of GroEL + GroES (7.7 A Resolution, emd_1180.map). We built a model for chain U correponding to protein 2C7D.pdb. This chain contains 97 residues and 4 distinct strands. Attached is our best model after the first round of Rosetta refinement. It exhibits a rmsd to native of 5.6 A, with a rmsd of 2.5 A over strand residues only. This result is very promising, especially because we have a very low rmsd over SSE-residues and we also expect the two subsequent Rosetta refinment rounds to improve the results further.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



Images and screenshots


Representative Image: 2C7DU_model_vs_native_v1.png

Screenshots and other example images:

Submission Details

Submission Title

model for 2C7DU

Submission Authors

  • Steffen Lindert
  • Tommy Hofmann
  • Nils Woetzel
  • Jens Meiler

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

Submission Comments

We developed an algorithm, EM-Fold, that predicts secondary structure elements from the primary sequence of the protein and folds these into identified regions corresponding to secondary structure in the density map. So for the purpose of this challenge we assumed that the provided density maps had been segmented into small density maps that only contain the individual chains of the proteins. We then identify positions of secondary structure elements in the map. Then EM-Fold (S. Lindert et al., Structure 17, 990 (Jul 15, 2009)) was used to assemble predicted SSEs into these density rods and refine positions of SSEs in these density rods. Finally Rosetta (F. DiMaio et al., J Mol Biol 392, 181 (Sep 11, 2009)) was used to build loops and side chains as well as refine further the best scoring models from EM-Fold. For this a three step protocol was used that identified the regions that agree least with density and then rebuilds coordinated for these. Due to time constraints for the submission of initial results we already submitted the Rosetta models after the first of the three iterative steps of refinement. We report rmsds of our models to the native chain (over full lenght protein and over the helical residues only).

We worked on map of GroEL + GroES (7.7 A Resolution, emd_1180.map). We built a model for chain U correponding to protein 2C7D.pdb. This chain contains 97 residues and 4 distinct strands. Attached is our best model after the first round of Rosetta refinement. It exhibits a rmsd to native of 5.6 A, with a rmsd of 2.5 A over strand residues only. This result is very promising, especially because we have a very low rmsd over SSE-residues and we also expect the two subsequent Rosetta refinment rounds to improve the results further.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



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