Predicting Protein Interactions by Brownian Dynamics Simulations

<table>Representation of the real (standard) and the soft (smoothed) van der Waals potential used in this work. Soft potential has the effect of widening the region of maximum affinity at <svg height="7.1875" id="M9" style="vertical-align:-0.13794pt" version="1.1" viewbox="0 0 7.6875 7.1875" width="7.6875" xmlns="http://www.w3.org/2000/svg">
<g transform="matrix(1.25,0,0,-1.25,0,7.1875)">
<g transform="translate(72,-66.25)">
<text transform="matrix(1,0,0,-1,-71.95,66.44)">
<tspan style="font-size: 12.50px; " x="0" y="0">𝜀</tspan>
</text>
</g>
</g>
</svg> and also reduces the potential energy at <svg height="10.9125" id="M10" style="vertical-align:-0.17555pt" version="1.1" viewbox="0 0 33.700001 10.9125" width="33.700001" xmlns="http://www.w3.org/2000/svg">
<g transform="matrix(1.25,0,0,-1.25,0,10.9125)">
<g transform="translate(72,-63.27)">
<text transform="matrix(1,0,0,-1,-71.95,63.5)">
<tspan style="font-size: 12.50px; " x="0" y="0">𝑟</tspan>
<tspan style="font-size: 12.50px; " x="8.5645552" y="0">=</tspan>
<tspan style="font-size: 12.50px; " x="20.604944" y="0">0</tspan>
</text>
</g>
</g>
</svg> to a finite value.</table>

BioMed Research International

Predicting Protein Interactions by Brownian Dynamics Simulations

Figure 3