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Protein design
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====Monte Carlo and simulated annealing==== Monte Carlo is one of the most widely used algorithms for protein design. In its simplest form, a Monte Carlo algorithm selects a residue at random, and in that residue a randomly chosen rotamer (of any amino acid) is evaluated.<ref name="voigt00" /> The new energy of the protein, <var>E</var><sub>new</sub> is compared against the old energy <var>E</var><sub>old</sub> and the new rotamer is ''accepted'' with a probability of: : <math> p=e^{-\beta(E_{\text{new}}-E_{\text{old}}))},</math> where <var>β</var> is the [[Boltzmann constant]] and the temperature <var>T</var> can be chosen such that in the initial rounds it is high and it is slowly [[simulated annealing|annealed]] to overcome local minima.<ref name="samish11">{{cite journal|last=Samish|first=I|author2=MacDermaid, CM |author3=Perez-Aguilar, JM |author4= Saven, JG |title=Theoretical and computational protein design.|journal=Annual Review of Physical Chemistry|year=2011|volume=62|pages=129β49|pmid=21128762|bibcode= 2011ARPC...62..129S |doi= 10.1146/annurev-physchem-032210-103509}}</ref>
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