| 3Drefine: an interactive web server for efficient protein structure refinement D Bhattacharya, J Nowotny, R Cao, J Cheng Nucleic acids research 44 (W1), W406-W409, 2016 | 405 | 2016 |
| 3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic‐level energy minimization D Bhattacharya, J Cheng Proteins: Structure, Function, and Bioinformatics 81 (1), 119-131, 2013 | 225 | 2013 |
| CONFOLD: Residue‐residue contact‐guided ab initio protein folding B Adhikari, D Bhattacharya, R Cao, J Cheng Proteins: Structure, Function, and Bioinformatics 83 (8), 1436-1449, 2015 | 184 | 2015 |
| DeepQA: improving the estimation of single protein model quality with deep belief networks R Cao, D Bhattacharya, J Hou, J Cheng BMC bioinformatics 17, 1-9, 2016 | 170 | 2016 |
| QAcon: single model quality assessment using protein structural and contact information with machine learning techniques R Cao, B Adhikari, D Bhattacharya, M Sun, J Hou, J Cheng Bioinformatics 33 (4), 586-588, 2017 | 94 | 2017 |
| Large-scale model quality assessment for improving protein tertiary structure prediction R Cao, D Bhattacharya, B Adhikari, J Li, J Cheng Bioinformatics 31 (12), i116-i123, 2015 | 65 | 2015 |
| i3Drefine software for protein 3D structure refinement and its assessment in CASP10 D Bhattacharya, J Cheng PloS one 8 (7), e69648, 2013 | 65 | 2013 |
| UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling D Bhattacharya, R Cao, J Cheng Bioinformatics 32 (18), 2791-2799, 2016 | 44 | 2016 |
| QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks MH Shuvo, S Bhattacharya, D Bhattacharya Bioinformatics 36 (Supplement_1), i285–i291, 2020 | 33 | 2020 |
| refineD: improved protein structure refinement using machine learning based restrained relaxation D Bhattacharya Bioinformatics 35 (18), 3320-3328, 2019 | 32 | 2019 |
| ConEVA: a toolbox for comprehensive assessment of protein contacts B Adhikari, J Nowotny, D Bhattacharya, J Hou, J Cheng BMC bioinformatics 17, 1-12, 2016 | 28 | 2016 |
| De novo protein conformational sampling using a probabilistic graphical model D Bhattacharya, J Cheng Scientific reports 5 (1), 16332, 2015 | 28 | 2015 |
| DeepRefiner: High-accuracy protein structure refinement by deep network calibration MH Shuvo, M Gulfam, D Bhattacharya Nucleic Acids Research 49 (W1), W147-W152, 2021 | 25 | 2021 |
| Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11 R Cao, D Bhattacharya, B Adhikari, J Li, J Cheng Proteins: Structure, Function, and Bioinformatics 84, 247-259, 2016 | 25 | 2016 |
| An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 C Keasar, LJ McGuffin, B Wallner, G Chopra, B Adhikari, D Bhattacharya, ... Scientific reports 8 (1), 9939, 2018 | 23 | 2018 |
| Modeling SARS‐CoV2 proteins in the CASP‐commons experiment A Kryshtafovych, J Moult, et al. PROTEINS : Structure, Function, and Bioinformatics, 2021 | 19 | 2021 |
| The MULTICOM protein tertiary structure prediction system J Li, D Bhattacharya, R Cao, B Adhikari, X Deng, J Eickholt, J Cheng Protein Structure Prediction, 29-41, 2014 | 18 | 2014 |
| Generating field-based inventory of earthquake-induced landslides in the Himalayas-an aftermath of the 18 September 2011 Sikkim Earthquake S Ghosh, I Chakraborty, D Bhattacharya, A Bora, A Kumar Indian Journal of Geosciences 66 (1), 27-38, 2012 | 16 | 2012 |
| DisCovER: distance‐and orientation‐based covariational threading for weakly homologous proteins S Bhattacharya, R Roche, B Moussad, D Bhattacharya Proteins: Structure, Function, and Bioinformatics 90 (2), 579-588, 2022 | 14 | 2022 |
| Recent advances in protein homology detection propelled by inter-residue interaction map threading S Bhattacharya, R Roche, MH Shuvo, D Bhattacharya Frontiers in Molecular Biosciences 8, 643752, 2021 | 14 | 2021 |
