The Side Effects of Small Molecule Drugs: Connecting Network and Atomistic Modeling

Master's Thesis


Systems 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.


Attribute NameValues
  • etd-07032011-102927

Author Yao Shen
Advisor Nitesh Chawla
Contributor Jesus A. Izaguirre, Committee Member
Contributor Nitesh Chawla, Committee Chair
Contributor Olaf Wiest, Committee Member
Degree Level Master's Thesis
Degree Discipline Computer Science and Engineering
Degree Name MSCSE
Defense Date
  • 2011-05-19

Submission Date 2011-07-03
  • United States of America

  • systems biology

  • network

  • drug discovery

  • molecular modeling

  • docking

  • side effect

  • molecular descriptor

  • University of Notre Dame

  • English

Record Visibility Public
Content License
  • All rights reserved

Departments and Units


Please Note: You may encounter a delay before a download begins. Large or infrequently accessed files can take several minutes to retrieve from our archival storage system.