Protein Structure Prediction and Folding
Mandatory reading
Extra
Slides
Videos
- Ab Initio Protein Folding
- CASP
- Molecular mechanics for protein folding
- Foldin@home
- Vijay Pande
- Protein Folding Models
- Rosetta
- Rosetta HR
- Rosetta@home
- Contact Predictions
- The protein folding revolution
- Protein Structure Prediction Lecture
Audio
Please explain why the free energy landscape is L shape and the reason behind no core nucleation.
Please elaborate the different dimension again e.g. lattice, fragments and etc. in “protein folding model” video
Please explain the graph of “contact score for 1ctf decoy set” again
Please explain direct and indirect effects again ( from Spatial proximity induces sequence coupling slide).
Please explain why if you have a contact in the middle, it will have more contacts nearby? And what does “contact in the middle” means in actual protein structure prediction problem?
What does “convergence” mean in the context of Pipeline and Post-CASP?
Could you please go through the ppts (since there are 2 ppt it might not be enough time, so how about a summary instead?)?
Two general question:
In addition to homology modeling, why fragment-similarity (e.g. Rosetta) is used in protein prediction? Is it due to the unavailability of homology models?
Compared to Marks paper about de novo protein prediction based on sequence, which method is more trustworthy?
Questions about the slide:
1. In “L shape of protein folding”, what does “p” in x-axis stand for? I cannot hear it clearly from the video.
2. In Rosetta, why 50%?
3. What is small dihedral change in HR Rosetta?
4. The terms “global” and “local” exist ma
ny times in the lecture. (e.g. global minimum,” Local conformations precede and guide global conformations”, “native-like global properties”. Could you go through this 3 terms? What is their importance to protein structural prediction?
4. Could you explain the HB plot of contact maps with more details (e.g. color and position of dots, layer)
5. It seems that PonsC3 is an important concept of this lecture, but I did not find enough information in Internet. Could you explain it a bit in the lecture or provide some extra information?
Please go through everything that is important to understand for the exam.
THe PconsC3 manuscript pdf seems to be damaged and wont open on the Ubuntu machines