Publications

[11] Sumit Tarafder, Debswapna Bhattacharya
“RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation”, bioRxiv [PDF] [Source]

[10] Sumit Tarafder, Debswapna Bhattacharya
“PARSEbp: Pairwise Agreement-based RNA Scoring with Emphasis on Base Pairings”, Bioinformatics Advances, 2026. Impact Factor: 2.8 [PDF] [Source]

[9] Rahmatullah Roche, Sumit Tarafder, Debswapna Bhattacharya
“A protocol for single-sequence protein-RNA complex structure prediction using ProRNA3D-single”, STAR Protocols, 2026. Impact Factor: 1.3 [PDF] [Source]

[8] Rahmatullah Roche, Sumit Tarafder, Debswapna Bhattacharya
“Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models”, Cell Systems, 2025. Impact Factor: 7.7 [PDF] [Source]

[7] Sumit Tarafder, Debswapna Bhattacharya
“lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures”, Journal of Chemical Information and Modeling, Volume 64, Issue 22, Pages 8655–8664, 2024. Impact Factor: 5.7 [PDF] [Source]

[6] Sumit Tarafder, Rahmatullah Roche, Debswapna Bhattacharya
“The landscape of RNA 3D structure modeling with transformer networks”, Biology Methods and Protocols, Volume 9, Issue 1, Page 47, 02 July 2024. Impact Factor: 2.5 [PDF] [Source]

[5] Sumit Tarafder, Xinyu Wang, Rahmatullah Roche, Debswapna Bhattacharya
“Advances in Language-Model-Informed Protein–Nucleic Acid Binding Site Prediction”, Methods in Molecular Biology, protocol, Page 139-151, 03 July 2025. Impact Factor: 1.3

[4] Rahmatullah Roche, Sumit Tarafder, Parkesh Suseendran, Xiaofeng Wang, Debswapna Bhattacharya
“Protein–Protein Interaction Site Prediction via EquiPPIS and Its Application in Studying Viral Replication”, Protein Evolution: Methods and Protocols, Pages 225–235, November 2025. IF: 1.3

[3] Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Sumit Tarafder, Debswapna Bhattacharya
“EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks”, NAR, volume 52, Issue 5, Page e27, 21 March 2024. Impact Factor: 14.9 [PDF] [Source]

[2] Sumit Tarafder, Mazharul Islam, Swakkhar Shatabda, Atif Rahman
“Figbird: a probabilistic method for filling gaps in genome assemblies”, Bioinformatics, Volume 38, Issue 15, 1 August 2022, Pages 3717–3724. Impact Factor: 5.8 [PDF] [Source]

[1] Sumit Tarafder, Md. Toukir Ahmed, Sumaiya Iqbal, Md Tamjidul Hoque, M. Sohel Rahman
“RBSURFpred: Modeling Protein Accessible Surface Area in Real and Binary Space using Regularized and Optimized Regression”, Journal of Theoretical Biology, Volume 441, 12 Jan 2018, Pages 44 - 57. Impact Factor: 2.0 [PDF] [Source]