Publications

* indicates Bhattacharya's advisee; † indicates equal contribution
Citations to these papers in Google Scholar; the papers listed in PubMed; code/data freely available for various papers on GitHub

Preprints

  1. Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models
    Rahmatullah Roche*, Sumit Tarafder*, Debswapna Bhattacharya
    bioRxiv, 2023
    Abstract • PDF • GitHub
2024

  1. lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures
    Sumit Tarafder*, Debswapna Bhattacharya
    Journal of Chemical Information and Modeling, 10.1021/acs.jcim.4c01621, 2024
    Abstract • PDF • GitHub

  2. Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules
    Trevor Norton*, Debswapna Bhattacharya
    Journal of Molecular Biology, 2024
    Abstract • PDF

  3. EquiRank: improved protein-protein interface quality estimation using protein-language-model-informed equivariant graph neural networks
    Md Hossain Shuvo*, Debswapna Bhattacharya
    International Conference on Intelligent Biology and Medicine (ICIBM), 2024
    GitHub

  4. The landscape of RNA 3D structure modeling with transformer networks
    Sumit Tarafder*, Rahmatullah Roche*, Debswapna Bhattacharya
    Biology Methods and Protocols, 9 (1), bpae047, 2024
    Abstract • PDF • GitHub

  5. EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
    Rahmatullah Roche*, Bernard Moussad*, Md Hossain Shuvo*, Sumit Tarafder*, Debswapna Bhattacharya
    Nucleic Acids Research, 52 (5), e27-e27, 2024
    Abstract • PDF • GitHub • Presented at the 3DSIG COSI Track of ISMB 2024
2023

  1. The transformative power of transformers in protein structure prediction
    Bernard Moussad†*, Rahmatullah Roche†*, Debswapna Bhattacharya
    Proceedings of the National Academy of Sciences of the United States of America, 120 (32) e2303499120, 2023
    Abstract • PDF • GitHub

  2. 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 Computational Biology, 19(8): e1011435, 2023
    Abstract • PDF • GitHub

  3. PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries
    Md Hossain Shuvo*, Mohimenul Karim*, Rahmatullah Roche*, Debswapna Bhattacharya
    Bioinformatics Advances, 3 (1) vbad070, 2023
    Abstract • PDF • GitHub

  4. iQDeep: an integrated web server for protein scoring using multiscale deep learning models
    Md Hossain Shuvo*, Mohimenul Karim*, Debswapna Bhattacharya
    Journal of Molecular Biology, 435(14): 168057, 2023
    Abstract • PDF • Server

  5. Contact-Assisted Threading in Low-Homology Protein Modeling
    Sutanu Bhattacharya*, Rahmatullah Roche*, Md Hossain Shuvo*, Bernard Moussad*, Debswapna Bhattacharya
    Methods in Molecular Biology, 2627: 41-59, 2023
    Abstract • PDF
2022

  1. rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation
    Rahmatullah Roche*, Sutanu Bhattacharya*, Md Hossain Shuvo*, Debswapna Bhattacharya
    PROTEINS: Structure, Function, and Bioinformatics, 90(12): 2023-2034, 2022
    Abstract • PDF • GitHub

  2. DisCovER: distance- and orientation-based covariational threading for weakly homologous proteins
    Sutanu Bhattacharya*, Rahmatullah Roche*, Bernard Moussad*, Debswapna Bhattacharya
    PROTEINS: Structure, Function, and Bioinformatics, 90(2): 579-588, 2022
    Abstract • PDF • GitHub • Presented at the 3DSIG COSI Track of ISMB/ECCB 2021

  3. Guest Editorial for Selected Papers From BIOKDD 2021
    Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, Jake Chen
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(6): 3068 - 3069, 2022
    Abstract • PDF
2021

  1. DeepRefiner: high-accuracy protein structure refinement by deep network calibration
    Md Hossain Shuvo*, Muhammad Gulfam*, Debswapna Bhattacharya
    Nucleic Acids Research, Web Server Issue, 49(W1): W147-W152, 2021
    Abstract • PDF • Server • Presented at the Highlights Track of ACM-BCB 2022

  2. Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins
    Rahmatullah Roche*, Sutanu Bhattacharya*, Debswapna Bhattacharya
    PLOS Computational Biology, 17(2): e1008753, 2021
    Abstract • PDF • GitHub • Presented at the Highlights Track of ACM-BCB 2021

  3. Modeling SARS-CoV-2 proteins in the CASP-commons experiment
    Andriy Kryshtafovych et al.
    PROTEINS: Structure, Function, and Bioinformatics, 89(12): 1987-1996, 2021
    Abstract • PDF

  4. Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading
    Sutanu Bhattacharya*, Rahmatullah Roche*, Md Hossain Shuvo*, Debswapna Bhattacharya
    Frontiers Molecular Biosciences, 8: 643752, 2021
    Abstract • PDF • In memoriam of Cyrus Chothia

  5. Guest Editorial for the 20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021)
    Da Yan, Steve Qin, Debswapna Bhattacharya, Jake Chen, Mohammed J. Zaki
    ACM SIGKDD Conference on Knowledge Discovery & Data Mining (KDD), 4175-4176, 2021
    Abstract • PDF
2020

  1. 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
    Intelligent Systems for Molecular Biology (ISMB), 2020
    Bioinformatics, 36(S1): i285-i291, 2020
    Abstract • PDF • GitHub • Presented at the Proceedings Track of ISMB 2020

  2. PolyFold: an interactive visual simulator for distance-based protein folding
    Andrew McGehee*, Sutanu Bhattacharya†*, Rahmatullah Roche†*, Debswapna Bhattacharya
    PLOS ONE, 15(12): e0243331, 2020
    Abstract • PDF • GitHub • ACM-BCB 2020 Best Poster Award

  3. Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading
    Sutanu Bhattacharya*, Debswapna Bhattacharya
    Scientific Reports, 10: 2908, 2020
    Abstract • PDF

  4. SPECS: integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models
    Rahul Alapati*, Md Hossain Shuvo*, Debswapna Bhattacharya
    PLOS ONE, 15(2): e0228245, 2020
    Abstract • PDF • GitHub • Server
2019

  1. Does inclusion of residue-residue contact information boost protein threading?
    Sutanu Bhattacharya*, Debswapna Bhattacharya
    PROTEINS: Structure, Function, and Bioinformatics, 87(7): 596-606, 2019
    Abstract • PDF • Front Cover Article • Presented at the Highlights Track of ACM-BCB 2019

  2. refineD: improved protein structure refinement using machine learning based restrained relaxation
    Debswapna Bhattacharya
    Bioinformatics, 35(18): 3320-3328, 2019
    Abstract • PDF • Server • Presented at the Oral Presentation Track of GLBIO 2019
2018

  1. clustQ: Efficient Protein Decoy Clustering Using Superposition-free Weighted Internal Distance Comparisons
    Rahul Alapati*, Debswapna Bhattacharya
    ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), 307-314, 2018
    Abstract • PDF • Server • Presented at the Proceedings Track of ACM-BCB 2018

  2. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
    Chen Keasar, Liam McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giedo, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena lusarz, Rafal lusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popovi, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Odziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Foldit Players consortium, Silvia N. Crivelli
    Scientific Reports, 8: 9939, 2018
    Abstract • PDF
2017

  1. 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, Jianlin Cheng
    Bioinformatics, 33 (4): 586-588, 2017
    Abstract • PDF

  2. Assessing Predicted Contacts for Building Protein Three-Dimensional Models
    Badri Adhikari, Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng
    Methods in Molecular Biology, 1484: 115-126, 2017
    Abstract • PDF
2016

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

  2. 3Drefine: an interactive web server for efficient protein structure refinement
    Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng
    Nucleic Acids Research, Web Server Issue, 4 (W1): W406-W409, 2016
    Abstract • PDF • Server

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

  4. DeepQA: improving the estimation of single protein model quality with deep belief networks
    Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
    BMC Bioinformatics, 17: 495, 2016
    Abstract • PDF • Software

  5. ConEVA: a toolbox for comprehensive assessment of protein contacts
    Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
    BMC Bioinformatics, 17: 517, 2016
    Abstract • PDF • Software
2015

  1. De novo protein conformational sampling using a probabilistic graphical model
    Debswapna Bhattacharya, Jianlin Cheng
    Scientific Reports, 5: 16332, 2015
    Abstract • PDF • Server

  2. Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11
    Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng
    PROTEINS: Structure, Function, and Bioinformatics, 84(S1): 247-259, 2015
    Abstract • PDF • Server • Invited CASP Proceedings Article

  3. CONFOLD: Residue-residue contact guided ab initio protein folding
    Badri Adhikari, Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng
    PROTEINS: Structure, Function, and Bioinformatics, 83(8): 1436-1449, 2015
    Abstract • PDF • Server

  4. Large-scale model quality assessment for improving protein tertiary structure prediction
    Renzhi Cao, Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng
    Intelligence Systems for Molecular Biology & European Conference on Computational Biology (ISMB/ECCB), 2015
    Bioinformatics, 31(12): i116-i123, 2015
    Abstract • PDF • Server
2014

  1. The MULTICOM Protein Tertiary Structure Prediction System
    Jilong Li, Debswapna Bhattacharya, Renzhi Cao, Badri Adhikari, Xin Deng, Jesse Eickholt, Jianlin Cheng
    Methods in Molecular Biology, 1137: 29-41, 2014
    Abstract • PDF • Server
2013

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

  2. Protein Structure Refinement by Iterative Fragment Exchange
    Debswapna Bhattacharya, Jianlin Cheng
    ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), 106-114, 2013
    Abstract • PDF • Server

  3. A Contact-Assisted Approach to Protein Structure Prediction and Its Assessment in CASP10
    Badri Adhikari, Xin Deng, Jilong Li, Debswapna Bhattacharya, Jianlin Cheng
    Association for the Advancement of Artificial Intelligence (AAAI), 2013
    Abstract • PDF • Server

  4. 3Drefine: Consistent protein ptructure pefinement by optimizing hydrogen bonding network and atomic-level energy minimization
    Debswapna Bhattacharya, Jianlin Cheng
    PROTEINS: Structure, Function, and Bioinformatics, 81(1): 119-131, 2013
    Abstract • PDF • Server • Most Accessed Article

© Debswapna Bhattacharya,