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Representative Image: 3FICD_model_vs_native_v1.png

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Submission Details

Submission Title

model for 3FICD

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 length protein and over the helical residues only).

We worked on map of Thermus thermophilus (70S) ribosome (6.4 A Resolution, emd_5030.map). We built a model for chain D corresponding to protein 3FIC.pdb. This chain contains 208 residues and 5 distinct helices. Attached is our best model after the first round of Rosetta refinement. It exhibits a rmsd to native of 12.5 A, with a rmsd of 3.4 A over helix residues only. The rmsd over full length is not very good but the rmsd over helical residues is excellent. This illustrates that EM-Fold correctly assembles regions of high helical content, but Rosetta understandably has a very hard time building large missing regions of the protein that even contain some smaller strands that we didn't pick up.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



Images and screenshots


Representative Image: 3FICD_model_vs_native_v1.png

Screenshots and other example images:

Submission Details

Submission Title

model for 3FICD

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 length protein and over the helical residues only).

We worked on map of Thermus thermophilus (70S) ribosome (6.4 A Resolution, emd_5030.map). We built a model for chain D corresponding to protein 3FIC.pdb. This chain contains 208 residues and 5 distinct helices. Attached is our best model after the first round of Rosetta refinement. It exhibits a rmsd to native of 12.5 A, with a rmsd of 3.4 A over helix residues only. The rmsd over full length is not very good but the rmsd over helical residues is excellent. This illustrates that EM-Fold correctly assembles regions of high helical content, but Rosetta understandably has a very hard time building large missing regions of the protein that even contain some smaller strands that we didn't pick up.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



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