[Colloquium] Seminar Announcement: Predictions of Structures of Protein Interactions

[Ninfa Mayorga]

Computation Institute Presentation

Speaker: Daisuke Kihara, Department of Biological Sciences/Computer Science
Date: May 20, 2013
Time: 10:30 AM - 12:00 PM
Location: University of Chicago, Searle 240A, 5735 S. Ellis Ave.

Predictions of Structures of Protein Interactions

Protein-protein binding events mediate many important biological functions in a cell. To provide molecular view of interacting proteins, our group has been developing a series of methods for predicting protein docking interfaces as well as the three dimensional structure of protein docking complexes. In this presentation, first we will introduce a protein docking algorithm, LZerD. LZerD uses the 3D Zernike descriptor, a rotational invariant mathematical representation of protein surfaces, to detect shape complementarity of interaction sites. Then, I will introduce our methods for predicting docking interface regions in protein surfaces, which detects binding site specific mutation patterns (BindML). As a subsequent work, we have developed a protein docking algorithm, which uses imperfect predicted protein-protein docking interface information (PI_LZerD). Finally, we present Multi-LZerD, which can predict the structure of multiple docking proteins by combining pairwise docking prediction computed by LZerD and the EM-LZerD method that fit multiple component structures into a low-resolution electron microscopy maps.

References
Multi-LZerD: Multiple protein docking for asymmetric complexes. J. Esquivel-Rodriguez, Y.D. Yang, & D. Kihara Proteins: Structure, Function, and Bioinformatics, in press (2012)

Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. J. Esquivel-Rodriguez, & D. Kihara Journal of Physical Chemistry B, in press (2012)

Protein docking prediction using predicted protein-protein interface. B. Li & D. 
Kihara, BMC Bioinformatics, 13: 7 (2012)

A novel method for protein-protein interaction site prediction using phylogenetic substitution models. D. La & D. Kihara Proteins: Structure, Function, and Bioinformatics, 80: 126-141 (2012)

Protein-protein docking using region-based 3D Zernike descriptors. V. 
Venkatraman, Y.D. Yang, L. Sael & D. Kihara BMC Bioinformatics, 10: 407. (2009)

BIO
Daisuke Kihara is Associate Professor of Department of Biological Sciences and Department of Computer Science at Purdue University, West Lafayette, Indiana, USA. He received his Ph.D. degree from Kyoto University, Japan, in 1999. His research projects include protein docking, protein tertiary structure prediction, structure- and sequence-based protein function prediction, and computational drug design. He has published over 85 research papers and book chapters. His research projects are supported by fundings from the National Institutes of Health, the National Science Foundation, Eli Lilly, and Korean Research Foundation. In 2013, he was named University Faculty Scholar by Purdue University. His lab website is at http://kiharalab.org

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Daisuke Kihara
Department of Biological Sciences/Computer Science
Purdue University
West Lafayette, IN
dkihara at purdue.edu




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