Protein Structure Refinement by Iterative Fragment Exchange. - Debswapna Bhattacharya; Jianlin Cheng (BCB, 2013)

Automated protein structure refinement using i3Drefine software and its assessment in CASP10. - Debswapna Bhattacharya; Jianlin Cheng (BCB, 2013)

Large-scale model quality assessment for improving protein tertiary structure prediction. - Renzhi Cao; Debswapna Bhattacharya; Badri Adhikari; Jilong Li; Jianlin Cheng (Bioinform., 2015)

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling. - Debswapna Bhattacharya; Badri Adhikari; Jilong Li; Jianlin Cheng (Bioinform., 2016)

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. - Debswapna Bhattacharya; Renzhi Cao; Jianlin Cheng (Bioinform., 2016)

ConEVA: a toolbox for comprehensive assessment of protein contacts. - Badri Adhikari; Jackson Nowotny; Debswapna Bhattacharya; Jie Hou 001; Jianlin Cheng (BMC Bioinform., 2016)

DeepQA: improving the estimation of single protein model quality with deep belief networks. - Renzhi Cao; Debswapna Bhattacharya; Jie Hou 001; Jianlin Cheng (BMC Bioinform., 2016)

3Drefine: an interactive web server for efficient protein structure refinement. - Debswapna Bhattacharya; Jackson Nowotny; Renzhi Cao; Jianlin Cheng (Nucleic Acids Res., 2016)

QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. - Renzhi Cao; Badri Adhikari; Debswapna Bhattacharya; Miao Sun; Jie Hou 001; Jianlin Cheng (Bioinform., 2017)

clustQ: Efficient Protein Decoy Clustering Using Superposition-free Weighted Internal Distance Comparisons. - Rahul Alapati; Debswapna Bhattacharya (BCB, 2018)

Contact-assisted Protein Threading: An Evolving New Direction. - Sutanu Bhattacharya; Debswapna Bhattacharya (BCB, 2019)

How Effective is Contact-assisted Protein Threading? - Sutanu Bhattacharya; Debswapna Bhattacharya (BCB, 2019)

refineD: improved protein structure refinement using machine learning based restrained relaxation. - Debswapna Bhattacharya (Bioinform., 2019)

QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks. - Md Hossain Shuvo; Sutanu Bhattacharya; Debswapna Bhattacharya (Bioinform., 2020)

Hybridized distance- and contact- based hierarchical protein structure modeling using DConStruct. - Rahmatullah Roche; Sutanu Bhattacharya; Debswapna Bhattacharya (BCB, 2021)

20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021). - Da Yan 001; Steve Qin; Debswapna Bhattacharya; Jake Y. Chen; Mohammed J. Zaki (KDD, 2021)

DeepRefiner: high-accuracy protein structure refinement by deep network calibration. - Md Hossain Shuvo; Muhammad Gulfam; Debswapna Bhattacharya (Nucleic Acids Res., 2021)

Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins. - Rahmatullah Roche; Sutanu Bhattacharya; Debswapna Bhattacharya (PLoS Comput. Biol., 2021)

Guest Editorial for Selected Papers From BIOKDD 2021. - Da Yan 001; Zhaohui S. Qin; Debswapna Bhattacharya; Jake Y. Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction. - Rahmatullah Roche; Bernard Moussad; Md Hossain Shuvo; Debswapna Bhattacharya (PLoS Comput. Biol., 2023)

Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules. - Trevor Norton; Debswapna Bhattacharya (CoRR, 2024)

lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures. - Sumit Tarafder; Debswapna Bhattacharya (J. Chem. Inf. Model., 2024)

To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era. - Sriniketh Vangaru; Debswapna Bhattacharya (Briefings Bioinform., 2025)