BASIL2022GV3HDT: Difference between revisions

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== Docking==

We used POCASA to determine potential binding pockets within our protein and PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to actually bind dCMP to 3HDT. Then PyMOL was used to visualize the binding pockets and dCMP in the protein. This <scene name='90/904996/Binding_pockets/1'>binding pocket</scene> (in purple) is a potential pocket the substrate dCMP may bind to in the protein, 3HDT. However, this area was where dCMP binded with the highest affinity in PyRx. The ~~amino acids interacting with the substrate within that area are <scene name='90/904996/H-bonds/1'>Lys146 and Leu 202</scene> which interact with dCMP by hydrogen bonds. Also, there are other~~ <scene name='90/904996/Hydrophobic_interactions/1'>amino acids</scene> (Gly21, Ser22, Gly23, Val27, Thr 142, Gln149, Arg150, Thr197, Leu200, Thr201) that help hold the substrate in place in the protein.

We used POCASA to determine potential binding pockets within our protein and PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to actually bind dCMP to 3HDT. Then PyMOL was used to visualize the binding pockets and dCMP in the protein. This <scene name='90/904996/Binding_pockets/1'>binding pocket</scene> (in purple) is a potential pocket the substrate dCMP may bind to in the protein, 3HDT. However, this area was where dCMP binded with the highest affinity in PyRx. The <scene name='90/904996/Hydrophobic_interactions/1'>amino acids</scene> (Gly21, Ser22, Gly23, Val27, Thr 142, Gln149, Arg150, Thr197, Leu200, Thr201) interact within that area to help hold the substrate in place in the protein with hydrophobic interactions. Also, there are two amino acids <scene name='90/904996/H-bonds/1'>Lys146 and Leu 202</scene> that interact with dCMP with hydrogen bonds. However, these results may not be as accurate because during the docking process on PyRx, we were unsuccessful in getting the program to recognize where the ATP was bonded in the protein when docking our substrate.

However, these results may not be as accurate because during the docking process on PyRx, we were unsuccessful

[[Image:POCASA 3hdt image 2.png | 500px| center | thumb| Predicted binding pockets for 3HDT represented by the white stippling.]]

BASIL2022GV3HDT: Difference between revisions

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@@ Line 36: / Line 36: @@
 == Docking==
-We used POCASA to determine potential binding pockets within our protein and PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to actually bind dCMP to 3HDT. Then PyMOL was used to visualize the binding pockets and dCMP in the protein. This <scene name='90/904996/Binding_pockets/1'>binding pocket</scene> (in purple) is a potential pocket the substrate dCMP may bind to in the protein, 3HDT. However, this area was where dCMP binded with the highest affinity in PyRx. The amino acids interacting with the substrate within that area are <scene name='90/904996/H-bonds/1'>Lys146 and Leu 202</scene> which interact with dCMP by hydrogen bonds. Also, there are other <scene name='90/904996/Hydrophobic_interactions/1'>amino acids</scene> (Gly21, Ser22, Gly23, Val27, Thr 142, Gln149, Arg150, Thr197, Leu200, Thr201) that help hold the substrate in place in the protein.
+We used POCASA to determine potential binding pockets within our protein and PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to actually bind dCMP to 3HDT. Then PyMOL was used to visualize the binding pockets and dCMP in the protein. This <scene name='90/904996/Binding_pockets/1'>binding pocket</scene> (in purple) is a potential pocket the substrate dCMP may bind to in the protein, 3HDT. However, this area was where dCMP binded with the highest affinity in PyRx. The <scene name='90/904996/Hydrophobic_interactions/1'>amino acids</scene> (Gly21, Ser22, Gly23, Val27, Thr 142, Gln149, Arg150, Thr197, Leu200, Thr201) interact within that area to help hold the substrate in place in the protein with hydrophobic interactions. Also, there are two amino acids <scene name='90/904996/H-bonds/1'>Lys146 and Leu 202</scene> that interact with dCMP with hydrogen bonds. However, these results may not be as accurate because during the docking process on PyRx, we were unsuccessful in getting the program to recognize where the ATP was bonded in the protein when docking our substrate.
-However, these results may not be as accurate because during the docking process on PyRx, we were unsuccessful
 [[Image:POCASA 3hdt image 2.png | 500px| center | thumb| Predicted binding pockets for 3HDT represented by the white stippling.]]