Date of Award

2017

Publisher

North Dakota State University

Document Type

Thesis

Degree Awarded

Master of Science (MS)

Program

Genomics and Bioinformatics

Department

Plant Sciences

College

Agriculture, Food Systems and Natural Resources

Faculty Advisor

Yan, Changhui

Description

Protein-ligand docking is a structure-based computational method, which is used to predict the small molecule binding modes and binding affinities with protein receptors. The goals of this study are to compare the docking performances of different software and apply the docking method to predict how protein fatty acid desaturase 1 (FADS1) interact with ligands. Two docking software, Discovery Studio and AutoDock, are used for docking comparison of 195 protein-ligand complexes from PDBind dataset. AutoDock performs a little bit better than Discovery Studio on the docking percentage, which is the percent of the docked complexes out of 195. On the other hand, Discovery Studio has a higher accuracy (successfully docked complexes, within 5 RMSD of the native complex structures) than AutoDock. The interaction between FADS1 and Sesamin shows a similar pattern comparing to the interaction between a homolog of FADS1 and a ligand shown in a PDB structure (PDB id 1EUE).

Rights

NDSU policy 190.6.2

Rights Link

https://www.ndsu.edu/fileadmin/policy/190.pdf

Handle Identifier

https://hdl.handle.net/10365/28365

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