Placeholder image of a protein
Icon representing a puzzle

662: Blind Electron Density 4

Closed since over 13 years ago

Advanced Overall Prediction Electron Density

Summary

Created
December 20, 2012
Expires
Max points
100
Description

This is our fourth electron density puzzle with real data. Like our previous puzzles, we were able to pinpoint which regions belong to a single copy, though the density itself is less clear. Try to fit the protein into the density to get the best score! Secondary Structure Predictions are posted in the puzzle comments.

Top groups

  1. Avatar for Team Germany 21. Team Germany 1 pt. 0
  2. Avatar for Atheists, Skeptics, & Humanists 22. Atheists, Skeptics, & Humanists 1 pt. 0
  3. Avatar for DSN @ Home 23. DSN @ Home 1 pt. 0
  4. Avatar for null pointer exception 24. null pointer exception 1 pt. 0
  1. Avatar for ViJay7019 141. ViJay7019 Lv 1 5 pts. 519
  2. Avatar for Rhyslarn 142. Rhyslarn Lv 1 5 pts. 506
  3. Avatar for parsnip 143. parsnip Lv 1 5 pts. 495
  4. Avatar for Kevonni 144. Kevonni Lv 1 5 pts. 494
  5. Avatar for telesphore4 145. telesphore4 Lv 1 4 pts. 490
  6. Avatar for monkry 146. monkry Lv 1 4 pts. 477
  7. Avatar for kmf1016 147. kmf1016 Lv 1 4 pts. 465
  8. Avatar for jbyram2 148. jbyram2 Lv 1 4 pts. 465
  9. Avatar for Merf 149. Merf Lv 1 4 pts. 452
  10. Avatar for Savas 150. Savas Lv 1 4 pts. 439

Comments

beta_helix Staff Lv 1

Here is the sequence logo predicted by the SAM server.

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the amino acid Leucine at residue 37 is highly predicted to be part of a sheet. However, the Valines at residues 6-7 & 97 have an equal probability of being anything.

bertro Lv 1

I believe it is possible to improve this density cloud clarity:

1) The current density map seems to have been saved with a step of 2 (judging by the rough angles of the blobs) giving us a much rougher image to work with than with a step of 1.

2) Plus some dust cleaning (removing small blobs) would also greatly enhance our ability to navigate and distinguish the shape of the protein.

Please, could you re-submit the puzzle with a smoother/cleaner density cloud?

Thanks

grogar7 Lv 1

This puzzle seems to have disappeared from my list of available science puzzles. It is not supposed to have expired for several hours. Explanation?