I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (Introduction to Protein Structure Prediction: Methods and Algorithms). Does anyone know whether I can find some code (say in C++, Java, or R) related to the prediction of protein structures? Or, do you know other good articles or books related to the statistics of the protein folding problem?

Thanks for the help.

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One of the quickest ways to get oriented on what is going in the world of protein folding and modeling is to look at the proceedings of the Critical Assessment of Structure Prediction (CASP). CASP is basically a contest, held every 2 years where anyone can use their algorithm to predict the 3D structure of a protein whose structure is known, but not publicly available.

Its been a few years since I reviewed them results much - it looks like this year was interesting, but a perennial winner has been Rosetta, which has turned into an edifice of many suites of software which each execute different tasks in protein folding and modeling.

Open source software is pretty hard to find in this field. The software is complex. It usually includes components of machine and statistical learning, molecular dynamics, specialized algorithms that build up the protein one residue at a time, others which manipulate blocks of the protein structure around in space, electrostatic calculations, you name it. In addition, the software, once it gives some sort of result is quite valuable. I don't think any of these suites has really been released. I know that Rosetta is available to use as a web service, but you have to apply for access to the source. I don't think its an easy thing to get.

Some of the most complicated components are available open source. Molecular modeling and molecular dynamics open source software is quite sophisticated. I think we need an open source protein folding suite open source. I think David Shortle's algorithms might be a candidate for such a suite as its not so complicated and it works in some cases.

This field is pretty obscure and difficult to get around in. There aren't any easy introductions that I know of. Protein structures are computationally expensive and painful to work with in terms of writing software. On the other hand protein folding that really works is a revolutionary breakthrough, at least equal to the impact of the development of computers as a technology.


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