<p> Modeling allows us to better interpret and understand our experiment. We used modeling to better understand how our proteins are binding to PFAS and their binding strengths. </p>
<br>
<h2> Docking </h2>
<hr>
<p>We used Autodock 4 to simulate the interactions between our proteins and ligands.We took enzyme models off of Protein Data Bank and PFAS models off of PubChem to use for our simulations. Docking was performed for two proteins and two forms of PFAS</p>
<ul>
<li> haloacid dehalogenase(1aq6) with perfluorooctanoic acid (PFOA) </li>
<li> haloacid dehalogenase(1aq6) with perfluorooctanesulfonic acid (PFOS) </li>
<li> fluoroacetate dehalogenase(3r40) with perfluorooctanoic acid (PFOA) </li>
<li> fluoroacetate dehalogenase(3r40) with perfluorooctanesulfonic acid (PFOS) </li>
</ul>
<p> Using Autodock 4, we find the optimal conformation to have the highest interactions between the enzyme and PFAS. From there, we took our docking results into Protein Data Bank’s Protein-Ligand Interaction Profiler to analyze the interactions between our enzymes and the PFAS. </p>
