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@@ -54,12 +54,12 @@ figcaption {
     </figure>
     <h4 style = "color:rgb(255, 255, 255)">Model of our engineered sequence is consistent with prior measurements of a disulfide bond</h4>
     <p>
-      While the AlphaFold [1] predictions are low confidence of the H-fibroin structure as a whole, the use of energy minimization and molecular 
-      dynamics [2,3,4] builds confidence in the quality of this output. Most importantly, our model suggests that key residue-specific interactions 
+      While the AlphaFold <a href="#ref1"><sup>[1]</sup></a> predictions are low confidence of the H-fibroin structure as a whole, the use of energy minimization and molecular 
+      dynamics <a href="#ref2"><sup>[2]</sup></a>,<a href="#ref3"><sup>[4]</sup></a>,<a href="#ref4"><sup>[7]</sup></a> builds confidence in the quality of this output. Most importantly, our model suggests that key residue-specific interactions 
       between L- and H-fibroin are preserved in our engineered sequences, relative to their native counterparts. A strong cysteine-cysteine disulfide 
       interaction between h- and L-fibroin is predicted to be preserved—for instance, the model suggests that the cysteine ~20 residues from the end 
       of our engineered H-fibroin and the cysteine between residues 150 and 200 of the L-fibroin are consistent with their expected relative positions 
-      and that they maintain the strong cysteine-cysteine disulfide interaction observed in existing caddisfly silk proteins.[5]
+      and that they maintain the strong cysteine-cysteine disulfide interaction observed in existing caddisfly silk proteins.<a href="#ref5"><sup>[5]</sup></a>
     </p>
     <p>
       In prior biochemical experiments on homologous l- and H-fibroin subunits in the silkworm Bombyx mori, performed by Tanaka et al., Cys-172 of 
@@ -71,13 +71,13 @@ figcaption {
       which facilitated a search for the specific residues involved in disulfide bonding (divide and conquer). The fragments containing cysteine residues 
       were deduced by sequencing, and peptide sequence analysis indicated which fractions formed disulfide bonds. Two iterations of chromatography were enough 
       to deduce that H-fibroin Cys-c1 and Cys-c4 forms an intramolecular disulfide bond, while <b>Cys-c20 forms an intermolecular disulfide linkage with Cys-172 
-      of the L-chain.</b> [7]
+      of the L-chain.</b> <a href="#ref7"><sup>[7]</sup></a>
     </p>
     <figure class="figure-container">
       <img src="https://static.igem.wiki/teams/4676/wiki/modeling/bombyx-fig5.gif" style="width: 40%; height: auto;" class="figure-img img-fluid">
       <figcaption class="figure-caption">Chromatography of the L-fibroin fractions and peptide sequence analysis, identifying the specific fractions containing 
         disulfide interactions (L2 and L7, which was further narrowed down to L7-2 in a re-chromatography). With the known amino acid sequence, the exact cysteine 
-        residues involved in disulfide bonding can be deduced. [7]</figcaption>
+        residues involved in disulfide bonding can be deduced. <a href="#ref7"><sup>[7]</sup></a></figcaption>
     </figure>
     <h4 style = "color:rgb(255, 255, 255)">A retained correlation between secondary structures and sequence composition</h4>
     <p>
@@ -98,7 +98,7 @@ figcaption {
       The model can be improved through the use of Monte Carlo protein folding and docking as provided in software such as pyRosetta, and through finer refinement with full-atom simulations using 
       AMBER force fields. Neither of these tools was used for our preliminary simulations due to hardware constraints and software limitations; however, they are ideal next steps to more rigorously 
       develop these silk protein models. One current plan of model development involves the inclusion of divalent ions (Ca2+) in the simulation to assess how these synthetic caddisfly silk protein 
-      structures may change as the interaction with ions is expected to cause the silk to harden into tough fibers [6].
+      structures may change as the interaction with ions is expected to cause the silk to harden into tough fibers. <a href="#ref6"><sup>[6]</sup></a>
     </p>
   </div>
 </div>