Analysis of SwissDock Docking Technique and Its Relation to The Advancement of BASIL Research
Start Date
29-4-2022 3:45 PM
Location
Alter Hall Poster Session 2 - 3rd floor
Abstract
The Basil Authentic Scientific Inquiry Lab (BASIL) curriculum consists of a series of 11 modules used to enhance undergraduate biochemistry lab experience. These modules were used to evaluate the function of proteins with known structures but unassigned functions. The main focus of this research relied on the use of a bioinformatics software called SwissDock. This software predicts possible binding models (BMs) and the estimated Gibbs free energy associated with the docking between each ligand and protein. The crystalline structure of each protein used were collected from the Protein Data Bank (PDB) and inserted into SwissDock. Ligands were prepared using ChemDraw by Dr. Stephen Mills. To analyze the accuracy of the software, 8 different ligands were docked into chymotrypsin and trypsin, two proteins of known function. For each protein, the BM with the lowest Gibbs free energy value was taken as the best BM. For chymotrypsin, tyrosine had the best BM. While for trypsin, lysine was the best. Both results were consistent with what is expected of these proteins—chymotrypsin acts on aromatics, and trypsin acts on lysine and arginine. After validation of the use of SwissDock for functional analysis, the process was repeated using unassigned protein 3H04. Docking results for each query, both assigned and unassigned, were visualized and evaluated using Chimera. Decanoate and tyrosine were found to bind with the lowest Gibbs free energy to the predicted active site of 3H04. Predictions of binding sites can be further verified with the use of the BASIL wet lab modules.
Analysis of SwissDock Docking Technique and Its Relation to The Advancement of BASIL Research
Alter Hall Poster Session 2 - 3rd floor
The Basil Authentic Scientific Inquiry Lab (BASIL) curriculum consists of a series of 11 modules used to enhance undergraduate biochemistry lab experience. These modules were used to evaluate the function of proteins with known structures but unassigned functions. The main focus of this research relied on the use of a bioinformatics software called SwissDock. This software predicts possible binding models (BMs) and the estimated Gibbs free energy associated with the docking between each ligand and protein. The crystalline structure of each protein used were collected from the Protein Data Bank (PDB) and inserted into SwissDock. Ligands were prepared using ChemDraw by Dr. Stephen Mills. To analyze the accuracy of the software, 8 different ligands were docked into chymotrypsin and trypsin, two proteins of known function. For each protein, the BM with the lowest Gibbs free energy value was taken as the best BM. For chymotrypsin, tyrosine had the best BM. While for trypsin, lysine was the best. Both results were consistent with what is expected of these proteins—chymotrypsin acts on aromatics, and trypsin acts on lysine and arginine. After validation of the use of SwissDock for functional analysis, the process was repeated using unassigned protein 3H04. Docking results for each query, both assigned and unassigned, were visualized and evaluated using Chimera. Decanoate and tyrosine were found to bind with the lowest Gibbs free energy to the predicted active site of 3H04. Predictions of binding sites can be further verified with the use of the BASIL wet lab modules.
