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Imagine if given an amino acid sequence, you could quickly calculate what the shape of the corresponding protein would be. You would be able to predict what effect a mutation would have on the shape of the protein. Switching just one glutamic acid with valine completely changes the shape of hemoglobin to the extent that people with this mutation are said to ...


16

Great question! Protein folding has been in open question for decades. Just recently, there's been a lot of discussion regarding DeepMind's AlphaFold project, which was discussed at length on our very own site here. My answer will be complementary to the one above, but the references I will provide will be closer to the physics side of the problem. First ...


10

Someone more familiar with the problem might have a better suggestion, but I recently came across Daniel B. Dix' notes on Mathematical Models of Protein Folding. This is not my field, so I won't guarantee correctness. However, to a layman at least, these notes seem well suited for someone with your background. The abstract reads We present an elementary ...


7

Preamble Since I don't know your specific background, this is a generic answer for any applied mathematician wishing to enter the field of protein folding. Not everything will apply specifically to you, and please don't feel offended if there's something I assume you don't already know or do! First of all, as a fellow mathematician (I was trained in ...


6

Keep in mind that many if not most proteins have multiple quasi-stable conformations, so their 3D structure is not actually a single conformation but rather a Markov matrix of conformations, with probabilities of a given conformation and probabilities of transition from each conformation to its neighbors varying according to temperature, pH, and other ...


6

Probably one of the important applications is Computer Aided Drug Discovery (CADD). If the protein structure could be accurately predicted, one could design protein-ligand docking on the binding pockets and run molecule dynamics simulations. In the lead identification process of a CADD, the starting point is normally be the experimental data for the crystal ...


6

Rosetta The protein modeling program Rosetta includes RNA structure prediction functionality. I think the most up-to-date tool is the FARFAR2 protocol. You can try it out through the Rosie FARFAR2 server.


3

In the Wikipedia link you provided, there are several packages capable to predict the RNA secondary structure already including pseudoknot prediction. Also, the links to the source code, executable or webserver are given. All of them start from sequence data. My suggestion is to use a service like CompaRNA that benchmark different methods/software used to ...


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