Sumit Tarafder

RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation

RNAbpFlow generates RNA 3D structures using base pair conditioning and SE(3)-equivariant flow matching, improving topology sampling in benchmarks.

PARSEbp: Pairwise Agreement-based RNA Scoring with Emphasis on Base Pairings

PARSEbp improves RNA structure scoring by integrating pairwise agreement and base pairing consistency, outperforming existing methods on CASP16 targets.

Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models

ProRNA3D-single predicts protein-RNA complex structures from single-sequence inputs, outperforming existing methods with limited evolutionary data.

lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures

lociPARSE is a new model that scores RNA 3D structures using a locality-aware attention mechanism, outperforming existing methods on multiple datasets.

EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks

EquiPNAS improves protein-nucleic acid binding site prediction using a pLM-informed equivariant graph neural network, outperforming existing methods on multiple datasets.

Figbird: A probabilistic method for filling gaps in genome assemblies

Figbird fills gaps in draft genome assemblies using a probabilistic method with EM algorithm, outperforming existing tools in accuracy and error reduction.