Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction

<table><tr><td><table class="algorithm" id="alg3"><tr><td colspan="2">(1) <span style="font-family:monospace">m</span><span style="font-family:monospace">utants.add</span>(<span style="font-family:monospace">conf</span>) </td></tr><tr><td colspan="2">(2) <b>foreach</b> 1 ≤ <span style="font-family:monospace">pos</span> ≤ <svg height="16.6625" id="M40" style="vertical-align:-3.56265pt" version="1.1" viewbox="0 0 71.400002 16.6625" width="71.400002" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
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q-97 56 -97 123q0 50 51 96q19 17 58 32.5t62 15.5q37 0 61 -18t24 -39z" id="x1D460"></path></g><g transform="matrix(.017,-0,0,-.017,6.437,12.162)"><path d="M391 364q0 -28 -20.5 -53.5t-50 -43.5t-70 -34t-73.5 -25t-68 -17v-29q0 -48 20 -81t65 -33q73 0 157 76l16 -23q-107 -113 -221 -113q-21 0 -40.5 6.5t-39 22t-31.5 47t-12 75.5q0 69 33.5 139.5t95.5 114.5q77 55 143 55q42 0 69 -24.5t27 -59.5zM313 350
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</svg> <b>do</b></td></tr><tr><td colspan="2">(3)  <svg height="7.9499998" id="M41" style="vertical-align:-0.1638pt" version="1.1" viewbox="0 0 43.5 7.9499998" width="43.5" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,7.675)"><path d="M383 397q0 -32 -35 -49q-12 -6 -23 8q-37 45 -84 45t-90 -71q-40 -65 -40 -167q0 -57 22 -86t59 -29q38 0 81.5 24.5t69.5 51.5l16 -21q-44 -53 -104 -84t-109 -31q-56 0 -89.5 41t-33.5 117q0 61 30 124t79 105q33 28 81 50.5t86 22.5q34 0 59 -15.5t25 -35.5z" id="x1D450"></path></g><g transform="matrix(.017,-0,0,-.017,11.673,7.675)"><path d="M1521 230h-1363l102 -147l-22 -15q-114 125 -185 187q71 62 185 187l22 -15l-102 -147h1363v-50z" id="x27F5"></path></g>
</svg><span style="font-family:monospace">apply</span><span style="font-family:monospace">O</span><span style="font-family:monospace">perator</span>(<span style="font-family:monospace">conf,</span> <span style="font-family:monospace">pos</span>) </td></tr><tr><td colspan="2">(4)  <span style="font-family:monospace">mutants</span><span style="font-family:monospace">.</span><span style="font-family:monospace">add</span>(<svg height="7.9499998" id="M42" style="vertical-align:-0.1638pt" version="1.1" viewbox="0 0 7.0250001 7.9499998" width="7.0250001" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,7.675)"><path d="M383 397q0 -32 -35 -49q-12 -6 -23 8q-37 45 -84 45t-90 -71q-40 -65 -40 -167q0 -57 22 -86t59 -29q38 0 81.5 24.5t69.5 51.5l16 -21q-44 -53 -104 -84t-109 -31q-56 0 -89.5 41t-33.5 117q0 61 30 124t79 105q33 28 81 50.5t86 22.5q34 0 59 -15.5t25 -35.5z" id="x1D450"></path></g>
</svg>) </td></tr><tr><td colspan="2">(5) <b>return</b>  <span style="font-family:monospace">bestConformation</span>(<span style="font-family:monospace">mutants</span>) </td></tr></table></td></tr></table>

The <i>pseudocode</i> of exhaustive mutation: <sans-serif>mutConf</sans-serif>(<sans-serif>conf</sans-serif>).

BioMed Research International

alg3

Algorithm 3

Algorithm 3: Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction 