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/sci/ - Science & Math

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File: 150 KB, 640x400, Hydrophobic bonds.png [View same] [iqdb] [saucenao] [google]
11345952 No.11345952 [Reply] [Original]

Are there any books that specialize in the hydrophobic bonds of proteins? Bonus points if the book talks about how this is essential to solve the protein folding problem. Bonus points if the book is geared towards computer programmers.

I try to read everything out there that might be helpful. That includes 2000 page books like "Braunwald's Heart Disease." While this book is the foremost authority in cardiology, only 2% of it was about proteins.

Yet, none of the books I've ever read have mentioned PyMol. Protein prediction is virtually impossible without protein visualization software. PyMol is the best protein visualization software I know of. Pic related.

In the pic, all the hydrophobic residues are shown in detail. Officially, the pertinent theory is called "hydrophobic collapse." This is misleading however. The term "hydrophobic interior" is much more appropriate. Without using PyMol, or a similar program, it would be almost impossible to appreciate this concept.

On Youtube, there's a lot about PyMol. Why don't books mention it? Images from PyMol would be very useful. The key to understanding proteins is all visual. Yet, no book I've read emphasizes this.

>> No.11345983

The only downside of PyMol is that it's like a 3 month subscription. Like a Netflix subscription, it can be renewed indefinitely though. Other alternatives include JMol and UCSF Chimera. As far as I can tell, they're not as good though.

I've seen Youtube videos on just about every protein visualization program out there. Sadly, no one shows a quick way to do what's in the OP image.

>> No.11346065
File: 147 KB, 862x399, protein biophysics.png [View same] [iqdb] [saucenao] [google]
11346065

Eirk Lindahl on Youtube has a lot of information on protein folding. He has a more concise, specialized, and relevant presentation than any other source I've found. Speaking of which, he just published a few new lectures this week.

>> No.11346125

If anyone is curious, I made the image in the OP image. It's not quick to make an image like that and that's not even counting measuring the distance non-polar hydrogens are from each other.

However, the resolution or algorithms used to clean up the data might be giving a false image. Intuitively some of the hydrogens appear so close to each other, that it probably not even possible.

>> No.11346316

>>11345983
Whoops the first 30 days, not 3 months are free.