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

<table><tr><td><table class="algorithm" id="alg4"><tr><td colspan="2">(1) <span style="font-family:monospace">c</span><span style="font-family:monospace">rossbred.add</span>(<span style="font-family:monospace">conf,conf</span><svg height="17.7125" id="M44" style="vertical-align:-0.0pt" version="1.1" viewbox="0 0 4.2750001 17.7125" width="4.2750001" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.012,-0,0,-.012,.062,9.488)"><path d="M227 744l-123 -338l-31 15l73 368q12 3 41.5 -8t36.5 -20z" id="x2032"></path></g>
</svg>) </td></tr><tr><td colspan="2">(2) <b>foreach</b>  1 ≤ <span style="font-family:monospace">pos</span> ≤ <svg height="16.6625" id="M45" 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">
<g transform="matrix(.017,-0,0,-.017,.062,12.162)"><path d="M352 391q0 -31 -27 -44q-14 -7 -24 6q-39 48 -84 48q-23 0 -39.5 -15t-16.5 -40q0 -43 73 -90q49 -32 70 -58t21 -57q0 -58 -62 -105.5t-129 -47.5q-40 0 -75.5 25t-35.5 52q0 28 32 46q7 4 15 3t11 -6q19 -31 48.5 -50.5t54.5 -19.5q34 0 54 19.5t20 42.5q0 43 -65 81
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
q0 26 -14.5 40.5t-37.5 14.5q-32 0 -44 -7q-82 -46 -104 -175q200 49 200 127z" id="x1D452"></path></g><g transform="matrix(.017,-0,0,-.017,13.475,12.162)"><path d="M474 429q-19 -69 -47 -222l-65 -347q-8 -49 0 -60t49 -16l26 -3l-4 -26l-246 -12l4 25l17 3q37 6 50 20.5t23 60.5l67 321h-2q-65 -79 -150 -138q-69 -47 -104 -47q-28 0 -48.5 32t-20.5 81q0 78 35 148t90 117q67 57 161 77q23 5 58 5q43 0 90 -15zM387 387
q-30 16 -75 16q-58 0 -92 -27q-49 -39 -78.5 -112t-29.5 -136q0 -34 8.5 -52.5t21.5 -18.5q40 0 109.5 63.5t103.5 115.5q16 53 32 151z" id="x1D45E"></path></g><g transform="matrix(.017,-0,0,-.017,21.821,12.162)"><path d="M559 163q-23 -66 -68 -163h-474l6 26q62 4 79.5 19.5t28.5 75.5l78 409q7 35 8.5 49t-8 25t-24 13t-51.5 5l5 28h266l-6 -28q-65 -5 -79.5 -18t-25.5 -74l-76 -406q-10 -57 14 -75q12 -13 96 -13q93 0 126 29q41 40 76 109z" id="x1D43F"></path></g><g transform="matrix(.017,-0,0,-.017,31.527,12.162)"><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
q0 26 -14.5 40.5t-37.5 14.5q-32 0 -44 -7q-82 -46 -104 -175q200 49 200 127z" id="x1D452"></path></g><g transform="matrix(.017,-0,0,-.017,38.565,12.162)"><path d="M495 86q-46 -47 -87 -72.5t-63 -25.5q-43 0 -16 107l49 210q7 34 8 50.5t-3 21t-13 4.5q-35 0 -109.5 -72.5t-115.5 -140.5q-21 -75 -38 -159q-50 -10 -76 -21l-6 8l84 340q8 35 -4 35q-17 0 -67 -46l-15 26q44 44 85.5 70.5t64.5 26.5q35 0 10 -103l-24 -98h2
q42 56 97 103.5t96 71.5q46 26 74 26q9 0 16 -2.5t14 -11.5t9.5 -24.5t-1 -44t-13.5 -68.5q-30 -117 -47 -200q-4 -19 -3.5 -25t6.5 -6q21 0 70 48z" id="x1D45B"></path></g><g transform="matrix(.017,-0,0,-.017,47.098,12.162)"><path d="M546 430q-14 -33 -37.5 -140t-38.5 -209q-29 -195 -156 -289q-29 -21 -70 -37t-78 -16q-62 0 -102.5 37t-40.5 69q0 27 26 48q19 15 25 -3q13 -43 46.5 -69t87.5 -26q55 0 83 21q29 22 50 65t43 140q14 64 29 163h-2q-55 -81 -149 -152q-59 -44 -102 -44q-23 0 -43.5 30
t-20.5 85q0 74 32.5 145.5t84.5 117.5q40 35 100 58.5t117 23.5q21 0 65 -8q30 -6 44 -6zM456 386q-40 16 -81 16q-29 0 -64 -13q-42 -17 -85 -97q-19 -36 -31.5 -86t-12.5 -86q0 -64 30 -64q20 0 52.5 21t60.5 52q74 81 95 123q26 62 36 134z" id="x1D454"></path></g><g transform="matrix(.017,-0,0,-.017,56.77,12.162)"><path d="M324 430l-26 -36l-112 -4l-55 -265q-13 -66 7 -66q13 0 44.5 20t50.5 40l17 -24q-38 -40 -85.5 -73.5t-87.5 -33.5q-50 0 -21 138l55 262h-80l-2 8l25 34h66l25 99l78 63l10 -9l-37 -153h128z" id="x1D461"></path></g><g transform="matrix(.017,-0,0,-.017,62.567,12.162)"><path d="M499 88q-41 -46 -83.5 -73t-68.5 -27q-41 0 -19 98l52 225q10 43 8 59.5t-16 16.5q-37 0 -112 -65t-117 -135q-14 -42 -38 -179q-36 -7 -75 -20l-7 8l127 594q8 40 2.5 49t-35.5 9h-35l5 25q36 3 71.5 13t56.5 18t25 8q11 0 3 -38l-88 -417h2q77 102 195 167q44 24 79 24
q61 0 30 -130l-52 -220q-8 -33 4 -33q8 0 31 14.5t43 33.5z" id="x210E"></path></g>
</svg>  <b>do</b></td></tr><tr><td colspan="2">(3)  <svg height="19.700001" id="M46" style="vertical-align:-1.59705pt" version="1.1" viewbox="0 0 61.262501 19.700001" width="61.262501" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,17.65)"><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,-.017,6.964,17.65)"><path d="M95 130q31 0 61 -30t30 -78q0 -53 -38 -87.5t-93 -51.5l-11 29q77 31 77 85q0 26 -17.5 43t-44.5 24q-4 0 -8.5 6.5t-4.5 17.5q0 18 15 30t34 12z" id="x2C"></path></g><g transform="matrix(.017,-0,0,-.017,13.661,17.65)"><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(.012,-0,0,-.012,20.575,9.488)"><path d="M227 744l-123 -338l-31 15l73 368q12 3 41.5 -8t36.5 -20z" id="x2032"></path></g>
<g transform="matrix(.017,-0,0,-.017,29.45,17.65)"><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">applyOperator</span>(<span style="font-family:monospace">conf,</span><span style="font-family:monospace"> </span><span style="font-family:monospace">conf</span><svg height="17.7125" id="M47" style="vertical-align:-0.0pt" version="1.1" viewbox="0 0 4.2750001 17.7125" width="4.2750001" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.012,-0,0,-.012,.062,9.488)"><path d="M227 744l-123 -338l-31 15l73 368q12 3 41.5 -8t36.5 -20z" id="x2032"></path></g>
</svg><span style="font-family:monospace">,</span> <span style="font-family:monospace">pos</span>)</td></tr><tr><td colspan="2">(4)  <span style="font-family:monospace">crossbred.add</span>(<svg height="19.700001" id="M48" style="vertical-align:-1.59705pt" version="1.1" viewbox="0 0 24.7875 19.700001" width="24.7875" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,17.65)"><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,-.017,6.964,17.65)"><path d="M95 130q31 0 61 -30t30 -78q0 -53 -38 -87.5t-93 -51.5l-11 29q77 31 77 85q0 26 -17.5 43t-44.5 24q-4 0 -8.5 6.5t-4.5 17.5q0 18 15 30t34 12z" id="x2C"></path></g><g transform="matrix(.017,-0,0,-.017,13.661,17.65)"><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(.012,-0,0,-.012,20.575,9.488)"><path d="M227 744l-123 -338l-31 15l73 368q12 3 41.5 -8t36.5 -20z" id="x2032"></path></g>
</svg>) </td></tr><tr><td colspan="2">(5) <b>return</b>  <span style="font-family:monospace">best2Conformations</span>(<span style="font-family:monospace">crossbred</span>) </td></tr></table></td></tr></table>

The <i>pseudocode</i> of exhaustive crossover: <sans-serif>crossConfs</sans-serif>(<sans-serif>conf</sans-serif>, <sans-serif>conf</sans-serif><svg height="17.7125" id="M43" style="vertical-align:-0.0pt" version="1.1" viewbox="0 0 4.2750001 17.7125" width="4.2750001" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.012,-0,0,-.012,.062,9.488)"><path d="M227 744l-123 -338l-31 15l73 368q12 3 41.5 -8t36.5 -20z" id="x2032"></path></g>
</svg>).

BioMed Research International

alg4

Algorithm 4

Algorithm 4: Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction 