Publications

Papers & preprints

In reverse-chronological order. My name is bolded within the author list on each entry.

2026

2026Nucleic Acids ResearchUnder review

OxView, oxCloud and nanobase: an interactive interface for simulation, analysis and sharing of DNA and RNA nanostructures.

Roy, S., Sikand, N., Sample, M., Evans, J., Haggenmueller, S., Kikla, A., Matthies, M., Šulc, P.

2026Frontiers in Neural CircuitsAccepted

Molecular Origami in Neuroscience: Noncanonical DNA Structures and Functional Nucleic Acids in Neural Regulation and Disease.

Roy, S., Pradhan, A. K., Jainarayanan, A. K.

2026bioRxivPreprint

DNA-templated Chiral Metamaterial Array as Information Bits.

Satyabola, D., Feng, S., Chopade, P., Prasad, A., Wang, L., Bamrah, N., Chen, L., Roy, S., Sakai, A., Wang, C., Sulc, P.

2026Nature ChemistryUnder review

Universal 3D Nanoscale Assembly with DNA Polycubes.

Diep, T.†, Liu, H.†, Evans, J., Matthies, M., Sample, M., Roy, S., Podbielski, D., Vaidyanathan, S., Williams, D., Kim, K., Kroc, L., Wang, H., Ke, Y., Hihath, J., Yan, H., Šulc, P.

2025

2025Journal of the American Chemical Society, 147(33), 29742–29755

DNA-Templated Spatially Controlled Proteolysis Targeting Chimera for Cyclin D1–CDK4/6 Complex Protein Degradation.

Zheng, R., Prasad, A., Satyabola, D., Xu, Y., Roy, S., Yan, Y., Sulc, P., Yan, H.

Coarse-grained oxDNA model of a spherical DNA origami, colored by root-mean-square fluctuation (RMSF) from 7.10 to 11.45 nm

2025Nature Communications

High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography.

Wisna, G. B. M., Sukhareva, D., Zhao, J., Satyabola, D., Matthies, M., Roy, S., Šulc, P., Yan, H., Hariadi, R. F.

2022

Scatter plot of CNN-predicted vs. ground-truth binding free energy (ΔG) for the PLAS-5k dataset, Pearson R = 0.947

2022Scientific Data, 9, 548

PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications.

Korlepara, D. B., Vasavi, C. S., Jeurkar, S., Pal, P., Roy, S., et al.

2020

Overlaid ribbon structures of the ZIKV NS1 protein β-ladder dimer in its unperturbed and disulfide-reduced states

2020Biophysical Journal, 119(8), 1525–1537

Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV.

Roy, P., Roy, S., Sengupta, N.