Secondary structure Prediction
Mandatory reading
- https://en.wikipedia.org/wiki/Protein_structure_prediction#Secondary_structure
- The PhD method
- The GOR method
Extra reading
Slides
Videos
- Protein Structure Prediction Introduction
- Amino Acid Properties
- Intro to Secondary Structure
- Secondary Structure Classification
- Physics of Secondary Structures
- Secondary Structure Prediction Introduction
- The GOR method
- The PhD method
- Secondary Structure Predictions Conclusions
The links for the PhD method and the GOR method under the mandatory reading do not work.
Folding recognition: what kinds of template?
Why prediction with too short secondary structure segments (in 1990s) could lead to bad beta strands prediction??
Explain PhD again and how it does to have correct length distribution? And How does that lead to better prediction?
THX.
– Can you please explain again the Ramachandran plot?
– Also about the secondary structure prediction with DSSP? (slide 20-22)
– In slide 26, 28 & 30 about amino acid preferences in α-helix, β-strand and coil, respectively, what do ‘bits’ on the y-axis and the numbers on the x-axis mean?
– With the Chou-Fasman method, how does it solve conflict between the helical and sheet-assignments?
– In slide 38 ‘Status of predictions in 1990’, the image is so stretched out and it was not discussed in the video. Can you please explain about that image example (and maybe provide the link for the original image, i.e. if it is not only an illustration)?
With all due respect, you spoke really fast and also somewhat inaudibly most of the time so it is really hard to understand. It would be greatly appreciated if you could speak slower and articulate more clearly in the future videos. Thank you!