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The Side Effects of Small Molecule Drugs: Connecting Network and Atomistic Modeling
thesis
posted on 2011-07-03, 00:00 authored by Yao ShenSystems biology is an emerging and multi-disciplinary research area that applies mathematical and computational models to analyze large-scale biological data. Systems biology is very promising to understand the mechanisms of drug reactions at the systems level as well as revolutionize the drug discovery process in the pharmaceutical industry, mainly focusing on the three aspects, drug combinations, drug repurposing and predicting drug side effects. My project aims at predicting new targets for old drugs, correlating targets and relating targets with side effects. The side effects of drugs are caused by on-target and off-target effects. Structurally similar drugs will bind to similar protein targets and cause similar side effects. Through data mining, hierarchical clustering and analyzing drug-target network, I have correlated targets based on their drugs similarities. The target similarity correlation provides a list of potential targets to be aware of when designing drugs for one target. I have also related targets with enriched rare side effects and determined new targets for the old drugs. This study combines both ligand-based similarity approach and atomistic modeling (docking) to validate the predictions.
History
Date Modified
2017-06-05Research Director(s)
Nitesh ChawlaCommittee Members
Jesus A. Izaguirre Olaf WiestDegree
- Master of Science in Computer Science and Engineering
Degree Level
- Master's Thesis
Language
- English
Alternate Identifier
etd-07032011-102927Publisher
University of Notre DameProgram Name
- Computer Science and Engineering
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