Finding Semirigid Domains in Biomolecules by Clustering Pair-Distance Variations

<table>Improvement of target function with number of clusters. Comparison between data from MD trajectory B4402 and randomly rearranged matrix elements <svg height="18.65" id="M166" style="vertical-align:-4.77652pt" version="1.1" viewbox="0 0 17.1875 18.65" width="17.1875" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.4)"><path d="M457 488l-30 -3q-17 148 -131 148q-53 0 -84.5 -34.5t-31.5 -82.5q0 -42 25.5 -72t74.5 -62l33 -22q63 -42 95 -85t32 -102q0 -84 -67 -137t-163 -53q-58 0 -113 22t-70 43l-4 152l27 4q4 -32 15 -62.5t31 -59.5t53.5 -47t76.5 -18q56 0 92 35t36 96q0 39 -25 70t-78 68
l-31 22q-32 23 -53.5 41.5t-45 57t-23.5 77.5q0 82 58 132.5t156 50.5q46 0 101 -17l18.5 -6t17 -6t8.5 -3q-4 -55 0 -147z" id="x1D446"></path></g>
<g transform="matrix(.012,-0,0,-.012,8.225,15.475)"><path d="M244 607q0 -25 -15.5 -43t-37.5 -18q-19 0 -32 13t-13 35q0 21 15 41t39 20q20 0 32 -14t12 -34zM222 91q-29 -33 -79 -68t-75 -35q-13 0 -19 7.5t-6 31t10 65.5l62 253q5 26 -1 26q-21 0 -72 -43l-13 24q43 40 91 68t71 28q30 0 10 -78l-71 -274q-8 -30 3 -30
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</svg>. Black graph “B4402” relates to matrix <svg height="12.2125" id="M167" style="vertical-align:-0.23827pt" version="1.1" viewbox="0 0 9.5749998 12.2125" width="9.5749998" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,11.825)"><path d="M484 692v-218h-28q-25 83 -70 130q-54 56 -123 56q-51 0 -80.5 -27t-29.5 -72q0 -37 21 -59q23 -25 82 -55q14 -8 68 -36q67 -34 80 -41q50 -28 79.5 -74.5t29.5 -101.5q0 -96 -69 -154q-68 -59 -179 -59q-61 0 -130 24q-30 10 -41 10q-23 0 -30 -34h-29v248h29
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</svg> obtained from a real MD-simulation, whereas the red graph “B4402 randomly rearranged” stems from a matrix with randomly rearranged elements (STDDVs).</table>

BioMed Research International

fig14

Figure 14

Figure 14: Finding Semirigid Domains in Biomolecules by Clustering Pair-Distance Variations 