My research interest
lies in Computational Biology and Bioinformatics. I am now working on the
following topics: protein structure alignment, protein structure prediction,
protein side-chain packing, protein-protein interaction prediction, DNA/protein
sequence search and biological network analysis.
Recent
Highlights
1. A poster on our paper
entitled Boosting Protein Threading
Accuracy won the Best Poster Award in RECOMB 2009 held in Tucson,
Arizona (May 17-21, 2009). RECOMB is one of the best conferences in the field
of Computational Biology and Bioinformatics.
2. The
following poster won the Best Poster Award in
CASP8 conference held in
J. DeBartolo, G. Hockey, F. Zhao, J. Peng,
A. Augustyn, A. Adhikar, J.
Xu, K. F. Freed and T. R. Sosnick.
Structure
prediction combining the template-based RAPTOR algorithm with the ItFix ab initio method.
3. My protein structure
prediction program RAPTOR ranked No.2-No.4 among
all automated programs in CASP8, according to several assessments (Grishin, McGuffin, Zhang) and the
CASP8 official ranking. The abstract
about RAPTOR in CASP8 is available at RAPTOR-CASP8.doc.
Please note that RAPTOR in CASP8 is very different from previous RAPTORs and there is only one RAPTOR participating in
CASP8. Here I give a list of people who contributed to RAPTOR in CASP8.
1) Jinbo Xu and his
students Jian Peng and Feng Zhao at TTI-Chicago: major contributors
2) Tobin Sosnick, Karl
Freed and Joe DeBartolo at U Chicago: the energy
function in the ab initio
folding module
3) Beckett W. Sterner and Shuaicheng
Li: two summer intern students involved in the very early stage of the ab initio folding module
4) Libo Yu: template database
generation
5) Brendan McConkey:
template database generation and one threading energy function
6) Xin Gao:
RAPTOR web server setup and running RAPTOR in the very early stage of CASP8
7) Ming Li: providing some computing resources
This new version RAPTOR
does not do any fragment assembly at all. We are working on a totally new web
server to provide free protein modeling service. The binary code of some
modules in the new version RAPTOR will also be available for download
gradually.