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Nucleic Acids Research|May 5, 2026
xBind: an integrated webserver for large language model-enabled cross-molecular protein binding site predictionXinyu Wang, Xingyue Feng, Sumit Tarafder, et al.Methods in Molecular Biology (Clifton, N.J.)|July 2, 2025
Advances in Language-Model-Informed Protein-Nucleic Acid Binding Site PredictionSumit Tarafder, Xinyu Wang, Rahmatullah Roche, et al.Methods in Molecular Biology (Clifton, N.J.)|November 1, 2025
Protein-Protein Interaction Site Prediction via EquiPPIS and Its Application in Studying Viral ReplicationRahmatullah Roche, Sumit Tarafder, Parkesh Suseendran, et al.Biorxiv : the Preprint Server for Biology|September 25, 2023
EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networksRahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, et al.Nucleic Acids Research|January 28, 2024
EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networksRahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, et al.Bioinformatics (Oxford, England)|February 14, 2019
refineD: improved protein structure refinement using machine learning based restrained relaxationDebswapna BhattacharyaProteins|August 29, 2012
3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimizationDebswapna Bhattacharya, Jianlin ChengBiorxiv : the Preprint Server for Biology|June 12, 2026
ORIGAMI: Orientation-Aware Graph Neural Network for Assessing Multimeric Interfaces of Protein Complex StructuresXinyu Wang, Debswapna BhattacharyaPlos One|July 30, 2013
i3Drefine software for protein 3D structure refinement and its assessment in CASP10Debswapna Bhattacharya, Jianlin ChengJournal of Molecular Biology|October 10, 2024
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomoleculesTrevor Norton, Debswapna BhattacharyaPageof 6