Structural Bioinformatics Study of Protein Interaction Network

1. Structural Bioinformatics Study of Protein Interaction Network Hui Lu, Bioengineering Primary Grant Support: NIH, DOL Protein-DNA complex: gene regulation DNA repair cancer treatment drug design gene therapy • Protein interacts with other biomolecules to perform a function: DNA/RNA, ligands, drugs, membranes, and other proteins. • A high accuracy prediction of the protein interaction network will provide a global understanding of gene regulation, protein function annotation, and the signaling process. • The understanding and computation of protein-ligand binding have direct impact on drug design. • Data mining protein structures • Molecular Dynamics and Monte Carlo simulations • Machine learning • Phylogenetic analysis of interaction networks • Gene expression data analysis using clustering • Binding affinity calculation using statistical physics • Developed the DNA binding protein and binding site prediction protocols that have the best accuracy available. • Developed transcription factor binding site prediction. • Developed the only protocol that predicts the protein membrane binding behavior. • Will work on drug design based on structural binding. • Will work on the signaling protein binding mechanism. • Will build complete protein-DNA interaction prediction package and a Web server.