Xue-Wen Chen photoXue-Wen Chen
Department of Electrical Engineering and Computer Science
University of Kansas


Computational Proteomics: Protein Interaction Prediction (2004-2007)

Proteins perform biological functions by interacting with other molecules. During the protein-protein interaction, the conserved domains physically interact with each other. Thus, understanding protein interactions at domain level gives detailed functional insights upon proteins that are either characterized or newly discovered. However, unlike protein-protein interactions that can be discovered by some high throughput technologies such as two-hybrid systems, domain-domain interactions largely remain unknown. This project addresses this issue by developing computational models to infer domain-domain interactions from protein-protein interactions; the model can then be used to validate and predict unknown protein interactions.

Dr. Chen and his research group first developed new computational models for inferring domain-domain interactions and for predicting protein-protein interactions. The newly developed computational models allowed them to:

  1. predict the undiscovered protein-protein interactions,
  2. identify protein domains in terms of protein functions, and
  3. validate the newly discovered protein-protein interactions through biological experiments or other means.

Second, they will develop an online system based on the computational models. This system will allow users to find the possible proteins that will interact with newly discovered proteins, validate protein-protein interactions, and identify protein domains.

Researchers have acquired protein-protein interaction data from several public domain databases, including the Database of Interacting Proteins, the Biomolecular Interaction Network Database and Human Protein Reference Database. The research group has written software scripts to retrieve from remote servers the sequences of proteins involved and to scan these sequences against the Pfam domain database to determine domains each protein may have. They have also designed and implemented a relational database to save collected data, protein sequences, and derived domain matching information. Work continues on the completion of the database collection and computational modeling methods.

Xue-Wen Chen received a CAREER award from the National Science Foundation in 2007. He was promoted to Professor of Electrical Engineering and Computer Science at the University of Kansas. Dr. Chen is now a professor in the Department of Computer Science and the Co-Director, Big Data & Analytics Group at Wayne State University, Detroit, MI.

Jianwen Fang photo

Dr. Jianwen Fang, co-investigator on the project, has a strong background and experience in structural bioinformatics and computer science, including software and database development. He and his team worked on the data acquisition of the project and developed an online system based on proposed computational models

Dr. Fang served as Director of the Applied Bioinformatics Laboratory from 2007-2013. He is now serving as a Computational Biologist at National Cancer Institute (NCI).