Protein Folding
I came across a paper on the pre-print archive: “Introduction to protein folding for physicists.” Proteins are polymers of amino acids and the sequence of these amino acids completely determine the native three dimensional structure. The human genome project gives us the sequences of all proteins in the human body. In theory it should be possible to study diseases like Alzheimer’s that are caused by the misfolding. Right?
Unfortunately, the combinatorial nature of the problem makes it impossible to do a brute force search. This paper is a decent introduction to the vocabulary of molecular biologists. The abstract:
[...] we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day sta- tus of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we phys- ically define the problem stating the assumptions behind this (commonly implicit) definition. [...]
The author recognizes the inadequacies of implicit solvent models. He also asks a key question: is kinetic information important for determining which minima is chosen. This was a similar question that I had while doing my docking project. Most docking algorithms right now only use static information.
References:
Introduction to protein folding for physicists, by Pablo Echenique. arXiv:0705.1845v1 [physics.bio-ph]
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