A Talk in Bioinformatics

Center for Bioinformatics Research Special Talk

Thursday, January 14, 2010

Dogwood Room, Indiana Memorial Union

3:00-4:00 p.m.

Admission Free



Yaoqi Zhou

IUPUI-School of Informatics

Director & Professor, Bioinformatics





From sequence to structure, to function, and back again: Integrating knowledge-based approaches with physical intuitions for protein folding, binding, and design





Abstract: Most biological activities are directed and/or regulated by proteins made of a gene-specified sequence of 20 amino-acid residue types. As a result, function or malfunction of specific proteins is responsible for almost all diseases. Proteins perform their function through their unique, self-assembled (folded) three-dimensional structures and through their specific binding to small molecules, to DNA/RNA (e.g. transcription factors that regulate gene expressions), or to other proteins (e.g. molecular recognition in signal transduction). Thus, how to predict the structure of a protein from its amino-acid sequence, discover the function from its structure and, then, design the sequence from its function or structure are the most essential problems in structural biology. In this talk, I will illustrate how the coupling of physical intuitions with learning from structural databases can go a long way toward untangling the complex relation between sequence, structure and function of proteins.

Biography: Trained as a theoretical physicist in a chemistry department, Dr. Zhou's research area moved to chemical engineering and computational biophysics during post-doctoral studies, and to bioinformatics when he became an independent researcher as an assistant professor at State University of New York at Buffalo in 2000.

His multidisciplinary training allows him to approach bioinformatic problems from the angle of physics. A recent example is the development of a knowledge-based energy function (called DFIRE) for proteins using the principle of physics rather than pure statistical information of protein structures. His group developed many freely available bioinformatic tools including SPARKS and SP3 for fold recognition and structure prediction, SPEM for multiple sequence alignment, SPINE for secondary and accessible surface area prediction, PINUP for binding-site prediction, MC2 for module identification from network of protein-protein interactions, and THUMBUP for topology prediction of transmembrane helical proteins.