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 Cagliari, Sardinia, Italy (Dec 3-7, 2008). CASP is the most prestigious competition in the field of protein structure prediction.

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.

Selected Publications (A Full List >>>)

Jian Peng and Jinbo Xu. Boosting Protein Threading Accuracy. RECOMB 2009. (A poster on this paper won the best poster award in RECOMB 2009.)

Feng Zhao, ShuaiCheng Li, Beckett W. Sterner and Jinbo Xu. Discriminative Learning for Protein Conformation Sampling. PROTEINS: Structure, Function and Bioinformatics, 2008.

Rohit Singh, Jinbo Xu and Bonnie Berger. Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood, accepted by RECOMB 2007.

Jinbo Xu, Feng Jiao and Bonnie Berger. A Parameterized Algorithm for Protein Structure Alignment. Accepted, RECOMB 2006. [pdf]

Rohit Singh, Jinbo Xu and Bonnie Berger. Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. Accepted, PSB 2006. URL: (The first two authors contribute equally to the paper.)

Jinbo Xu. Rapid Protein Side-Chain Packing via Tree Decomposition. RECOMB 2005. [ps][pdf] A software package based on this approach can be downloaded at SCATD. A full version of this paper appeared at the Journal of the ACM.

Jinbo Xu. Protein Fold Recognition by Predicted Alignment Accuracy. IEEE/ACM Trans. on Computational Biology and Bioinformatics, 2005. [ps][pdf]

Jinbo Xu, Daniel Brown, Ming Li and Bin Ma. Optimizing Multiple Spaced Seeds for Homology Search. Journal of Computational Biology, 2005. Accepted.[ps][pdf]

Jinbo Xu and Ming Li. Assessment of RAPTOR's Linear Programming Approach in CAFASP3, CASP5 (Fifth Critical Assessment of Structure Prediction) special issue, Proteins: Structure, Function and Genetics. Oct, 2003. (an invited paper, the only one voted by all the CASP5/CAFASP3 attendees according to novelty and performance.) [ps][pdf]

Jinbo Xu, Ying Xu, Dongsup Kim and Ming Li. RAPTOR: Optimal Protein Threading by Linear Programming, the inaugural issue, Journal of Bioinformatics and Computational Biology, April 2003.[ps] [pdf] A software package RAPTOR has been developed based on the method proposed in this paper. RAPTOR ranks first among all non-meta servers in CAFASP3 (Third Critical Assessment of Fully Automated Structure Prediction). RAPTOR also ranks third among all non-meta servers in CASP6 according to RAPTOR has been commercialized to BioinformaticsSolutions Inc., Waterloo, Canada and has been licensed to some pharmaceutical companies such as Merck.

Invited Talks

Protein threading by nonlinearly combining evolutionary and non-evolutionary information. The University of Minnesota, April 2009.

Protein threading by nonlinearly combining evolutionary and non-evolutionary information. MIT, March 2009.

Computer Algorithms for Structural Bioinformatics. INFORMS Annual Meeting, October 2008.

Computer Algorithms for Structural Bioinformatics. SIAM on Discrete Mathematics, June 2008.

Global Alignment of Multiple Protein Interaction Networks. UIC, April 2008.

Protein Conformation Sampling Using Conditional Random Fields. MIT, Feb 2008.

Knowledge-Based Protein Structure Prediction. TTI-Japan, April 2007.

Knowledge-Based Protein Structure Prediction. Inst of Comp Tech, Chinese Academy of Sciences, March 2007.

Knowledge-Based Protein Structure Prediction. Tsinghua University, March 2007.

A Parameterized Algorithm for Protein Structure Alignment. Waterloo, July 2006.

A Parameterized Algorithm for Protein Structure Alignment. MIT, May 2006.

Protein Structure Prediction. Northwestern University, May 2006.

A Parameterized Algorithm for Protein Structure Alignment. UIC, November 2005.

Protein Side-Chain Packing. Boston University, October, 2005.

Fast and Accurate Protein Side-Chain Prediction. DIMACS Workshop on Information Processing by Protein Structures in Molecular Recognition, DIMACS Center, CoRE Building, Rutgers University, June 13-14, 2005.

RAPTOR: protein threading by linear programming. SIAM minisymposium, SIAM Conference on Control and Its Applications. New Orleans, LA, July 11-14,2005.

ACE: consensus method to fold recognition. CASP6, Italy. Dec, 2004. (An invitation to our ACE group)

Protein Structure Prediction by Linear Programming. School of Medicine, University of Western Ontario, Oct, 2004.

Protein Structure Prediction. ICTS, University of Waterloo, 2003.