56

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 ...


17

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 ...


11

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 ...


9

If you know the program AMBER, There is an option where you write an input with the sequence that you want, automatically the program will build the two strands, and your output will be pdb format. Or You can use Avogadro program direct and you will write the sequence and the output will be XYZ format. The output


9

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 ...


7

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 ...


7

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.


5

If this is happening, I think there's a few reasons: Quantum physics in general is the science subject where the most precise agreement between theory and experiment exists. For example, the experimental work: Nature 588, pg 61–65 (2020) "Determination of the fine-structure constant with an accuracy of 81 parts per trillion", and a QED calculation ...


4

I'd start from An Introduction to Protein Structure Prediction which is part of a just published course Biological Modeling: A Free Online Course. The author of this course is also a mathematician by training. He co-authored a bioinformatics MOOC on Coursera, one of the best online lectures I listened to (in the meantime this MOOC became a series of smaller ...


3

For batch use, I recommend Open Babel which can translate fasta format DNA sequences into single or double-stranded DNA coordinates. (Indeed, it's used in Avogadro.) FASTA format: > DNA AATCT Then you can use something like this (documentation) obabel file.fasta -O file.pdb # output double-stranded obabel file.fasta -O file.pdb -a1 # output single-...


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 ...


1

Just basically collecting the comments here. The tutorials page for Martini states: The secondary structure of the protein influences both the selected bead types and bond/angle/dihedral parameters of each residue. So depending on the secondary structure, they may just alter how coarse the mapping is depending on how much detail is needed to emulate this ...


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