Publications

>> Google Scholar Citation Profile

 2017 


Renzhi Cao, Badri Adhikari, Debswapna Bhattacharya, Miao Sun, Jie Hou, Jianlin Cheng.
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques.
Bioinformatics, 33 (4): 586-588 (2017).
[PDF] [Support Information]



Badri Adhikari, Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng.
Assessing Predicted Contacts for Building Protein Three-Dimensional Models.
Springer, Methods in Molecular Biology, 1484: 115-126 (2017).
[PDF]

 2016 


Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng.
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.
Bioinformatics, 32 (18): 2791-2799 (2016).
[PDF] [Support Information] [Software]



Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng.
3Drefine: An Interactive Web Server for Efficient Protein Structure Refinement.
Nucleic Acids Research, Web Server Issue, 4 (W1): W406-W409 (2016).
[PDF] [Server]



Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng.
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.
Bioinformatics, 32 (13): 2059-2061 (2016).
[PDF] [Support Information] [Software]



Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng.
DeepQA: improving the estimation of single protein model quality with deep belief networks.
BMC Bioinformatics, 17:495 (2016).
[PDF] [Support Information] [Software]



Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng.
ConEVA: a Toolbox for Comprehensive Assessment of Protein Contacts.
BMC Bioinformatics, 17:517 (2016).
[PDF] [Server]

 2015 


Debswapna Bhattacharya, Jianlin Cheng.
De novo portein conformational sampling using a probabilistic graphical model.
Nature Scientific Reports, 5:16332 (2015).
[PDF] [Support Information] [Server]



Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng.
Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.
Proteins: Structure, Function, and Bioinformatics, 84(S1): 247-259 (2015).
[PDF] [Support Information] [Server]
CASP invited contribution



Badri Adhikari, Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng.
CONFOLD: Residue-residue contact guided ab initio protein folding.
Proteins: Structure, Function, and Bioinformatics, 83(8): 1436-1449 (2015).
[PDF] [Support Information] [Server]



Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng.
Large-scale model quality assessment for improving protein tertiary structure prediction.
Bioinformatics, 31(12): i116-i123 (2015).
[PDF] [Server]

 2014 


Jilong Li, Debswapna Bhattacharya, Renzhi Cao, Badri Adhikari, Xin Deng, Jesse Eickholt, Jianlin Cheng.
The MULTICOM Protein Tertiary Structure Prediction System.
Springer, Methods in Molecular Biology (2014).
[PDF] [Server]

 2013 


Debswapna Bhattacharya, Jianlin Cheng.
i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
PLOS ONE, 8(7): e69648 (2013).
[PDF] [Server]



Debswapna Bhattacharya, Jianlin Cheng.
Protein Structure Refinement by Iterative Fragment Exchange.
ACM-BCB 2013, Proceeding, 106-114 (2013).
[PDF] [Server]



Badri Adhikari, Xin Deng, Jilong Li, Debswapna Bhattacharya, Jianlin Cheng.
A Contact-Assisted Approach to Protein Structure Prediction and Its Assessment in CASP10.
AAAI 2013, Workshop (2013).
[PDF] [Server]



Debswapna Bhattacharya, Jianlin Cheng.
3Drefine: Consistent Protein Structure Refinement by Optimizing Hydrogen Bonding Network and Atomic Level Energy Minimization.
Proteins: Structure, Function, and Bioinformatics, 81(1): 119-131 (2013).
[PDF] [Support Information] [Server]
Top 10 most cited and the most accessed article in 2013 Proteins