id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
work_bwyl5aldazcytler7culcro2sm	Gonzalo S. Nido	Learning structural bioinformatics and evolution with a snake puzzle	2016	38	.pdf	application/pdf	16562	1566	61	Keywords Structural bioinformatics, Education, Protein folding, Statistical mechanics, Contact matrix, Protein structure alignment, Designability, Evolution, Contact order, Protein classification puzzle and the contact matrix representation of protein structures, and we propose a simple model structures, on which we propose computational exercises focused on evolutionary Contact matrices are also used as a simplified representation of real protein structures. We can define the sequence structure relationship within the contact energy model of contact interaction energies depend on the protein sequence as Uij =U(Ai,Aj), where Ai self avoiding walks on the cubic lattice or the contact matrices of real protein structures. Figure 6 Designability of selected structures for an increasing number of random sequences. energy where sequences with larger fitness are visited more often, in analogy with structures 2. Fitness evaluation We compute the folding free energy of the mutated sequence We simulate protein sequence evolution with structural constraints using a Monte Carlo	./cache/work_bwyl5aldazcytler7culcro2sm.pdf	./txt/work_bwyl5aldazcytler7culcro2sm.txt