BASIL2022GV3R8E: Difference between revisions
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[[Image:Workflow.png ]] | [[Image:Workflow.png ]] | ||
== Methods == | == Methods == | ||
As you can see in the workflow portion above, we used a variety of in silico tools such as BLASTp, Pfam, DALI, PyRx, and PyMol to help us generate a hypothesis for our uncharacterized proteins function. Using the FASTA sequence found in the Protein Data Bank file, we then were able to find similarities between 3r8e and other characterized proteins. While exploring the DALI database, a significant structural alignment hit was found with protein 3vov. Alignment and highly conserved amino acids can be seen below. | As you can see in the workflow portion above, we used a variety of in silico tools such as BLASTp, Pfam, DALI, PyRx, and PyMol to help us generate a hypothesis for our uncharacterized proteins function. Using the FASTA sequence found in the Protein Data Bank file, we then were able to find similarities between 3r8e and other characterized proteins. While exploring the DALI database, a significant structural alignment hit was found with protein 3vov. Alignment and highly conserved amino acids can be seen below. | ||
[[Image:DALI.png]] | [[Image:DALI.png]] | ||
These results along with supporting evidence from the other in silico tools allowed us to then conduct in silico docking experiments to further confirm our hypothesis. Below is a figure with the PyRx docking results of glucose and ATP with our protein. | These results along with supporting evidence from the other in silico tools allowed us to then conduct in silico docking experiments to further confirm our hypothesis. Below is a figure with the PyRx docking results of glucose and ATP with our protein. | ||
[[Image:PyRx.png]] | [[Image:PyRx.png]] | ||
The -5.1 kcal/mol value shows that our protein of interest hypothesis of a glucose kinase is strong. The confidence behind our in silico results allowed us to move into testing our hypothesis in vitro. | The -5.1 kcal/mol value shows that our protein of interest hypothesis of a glucose kinase is strong. The confidence behind our in silico results allowed us to move into testing our hypothesis in vitro. | ||
