807: De-novo Cryo-electron Density: Hand-folding Round

Closed since over 12 years ago

Summary

• Created: November 07, 2013
• Expires: November 15, 2013 at 12:00 UTC
• Max points: 100

Description

Try to fit this extended chain into the cryo-EM density cloud to gain points. This round only GUI scripts are allowed and sharing has been disabled. After this puzzle expires, the puzzle will be re-posted and LUA scripts and sharing will be allowed. You'll be able to load in your solutions from this puzzle and use scripting and sharing.

Top groups

• 21. Crunching Family 1 pt. 2,495
• 22. (no name) 1 pt. 2,298
• 23. Brony@Home 1 pt. 0
• 24. DSN @ Home 1 pt. 0
• 25. Team Schleswig-Holstein 1 pt. 0

Top soloists

• 91. robgee 15 pts. 4,834
• 92. phi16 15 pts. 4,830
• 93. tela 15 pts. 4,817
• 94. MurloW 14 pts. 4,801
• 95. guineapig 14 pts. 4,792
• 96. Tismitch 14 pts. 4,776
• 97. jamiexq 13 pts. 4,761
• 98. reefyrob 13 pts. 4,757
• 99. momadoc 13 pts. 4,757
• 100. smholst 12 pts. 4,729

Comments

[beta_helix]

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 Valines at residues 41-42 are highly predicted to be part of a helix. However, the Valines at residue 67 and 94 are predicted to be in sheets!

The above predictions are already on the starting model (based on the horizontal lines in the above figure).
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More info about Cryo-electron microscopy here:

en.wikipedia.org

Cryogenic electron microscopy

Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample solution is applied to a grid-mesh and plunge-frozen in liquid ethane or a mixture of liquid ethane and propane. While development of the technique began in the 1970s, recent advances in detector technology and software algorithms have allowed for the dete In...