Seminar

SEMINAR: Protein Structure Prediction and Clustering Using MUFOLD

Protein tertiary structures are essential for studying functions of proteins at molecular level. An indispensable approach for protein structure solution is computational prediction. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. To address this challenge, we developed MUFOLD, a hybrid method of using whole and partial template information along with graph-realization techniques for protein tertiary structure prediction. MUFOLD has demonstrated its effectiveness in CASPs and various applications. It is available through a Web server at http://mufold.org/prediction.php.

Furthermore, current protein structure prediction methods, including MUFOLD, often generate a large population of candidates (models), and then select near-native models through clustering. Existing structural model clustering methods are time consuming due to pairwise distance calculation between models. To address this issue, we developed a novel method for fast model clustering without losing the clustering accuracy, with a calculation time linearly proportional to the number of models. Our method has been implemented in a package named MUFOLD-CL, available at http://mufold.org/clustering.php. It can be used for other clustering problems as well.

Dong Xu
Department Chair and Professor, Department of Computer Science at University of Missouri

Dong Xu is  James C. Dowell professor and chair of the University of Missouri's Department of Computer Science. He earmed his doctorate at the University of Illinois in 1995 and completed two-years of postdoctoral work at the U.S. National Cancer Institute. He was a staff scientist at Oak Ridge National Laboratory until 2003 before joining the University of Missouri. His research focuses on bioinformatics and computational biology. He has published more than 230 papers. He is a recipient of 2001 R&D 100 Award, 2003 Federal Laboratory Consortium’s Award of Excellence in Technology Transfer, and 2010 Outstanding Achievement Award from International Society of Intelligent Biological Medicine. He serves as editor-in-chief of the “International Journal of Functional Informatics and Personalized Medicine” and associate editor-in-chief of “IEEE/ACM Transactions on Computational Biology and Bioinformatics.” 

When:
Wednesday, October 15, 2014, 3:00 pm - 4:00 pm
Where:
1124 Shelby Center
Contact:
Weikuan Yu
(334) 844-6330
wzy0005@auburn.edu