COLLOQUIUM
Department of Computer Science and Engineering
University of South Carolina

Prediction of Protein Structures and Modifications

Dong Xu

Department of Computer Science
University of Missouri

Date: March 28, 2012
Time: 1500-1600 (3pm-4pm)
Place: Swearingen 1A03 (Faculty Lounge)

Abstract

Computational prediction of protein often provides a useful basis for
understanding protein function, as a vast majority of proteins will
not be characterized experimentally. In this talk, I will illustrate
two examples of protein predictions, i.e., protein structure
prediction and protein posttranslational modification (PTM)
prediction, both of which are from protein sequence only. Towards
achieving more accurate and efficient structure prediction, we
developed a dramatically different framework from conventional methods
for protein structure prediction. This framework is implemented into a
software system MUFOLD. MUFOLD applies Multidimensional Scaling to
construct multiple models by sampling inter-residue spatial restraints
derived from alignments. It then evaluates models through clustering
and a machine learning-based scoring function, and iteratively
improves selected models based on model evaluation. MUFOLD
demonstrated its success in the community-wide experiment for protein
structure prediction CASP. We also developed an open-source software
system and the webserver MUSITE (http://musite.sourceforge.net;
http://musite.net) for large-scale PTM prediction. MUSITE applies a
machine learning approach that integrates local sequence similarities
to known PTM sites, protein disorder scores, and amino acid
frequencies. Cross-validation tests show that MUSITE significantly
outperforms existing tools for predicting PTM sites. We applied both
MUFOLD and MUSITE in studying various proteins in collaborations with
experimentalists.

Dr. Dong Xu is James C. Dowell Professor and Chair of the Computer
Science Department, with appointments in the Christopher S. Bond Life
Sciences Center and the Informatics Institute at the University of
Missouri-Columbia. He obtained his Ph.D. from the University of
Illinois, Urbana-Champaign in 1995 and did two-year postdoctoral work
at the US National Cancer Institute. He was a Staff Scientist at Oak
Ridge National Laboratory until 2003 before joining the University of
Missouri. Over the past seventeen years, he has published more than
130 scientific papers. Professor Xu is a recipient of the 2001 R&D 100
Award and the 2003 Federal Laboratory Consortium's Award of Excellence
in Technology Transfer. He is a member of the Editorial Board of
Current Protein and Peptide Science and Applied and Environmental
Microbiology. He is a standing member in the NIH Biodata Management
and Analysis Panel.