PUBLICATIONS

Selected Publications (Visit Google Scholar Profile for complete list)

📄 Multimodal cell maps as a foundation for structural and functional genomics (Nature, 2025)

📄 The molecular architecture of the nuclear basket. Singh*, Soni*, Hutchings* et. al. Cell 2024

📄 COCONUT: An analysis of coiled-coil regions in proteins. Soni and Madhusudhan, BioRxiv 2024

📄 Methods for molecular modeling of protein complexes, Methods in Mol. Biol. 2021.

📄 Predicting and designing therapeutics against the Nipah virus, PLOS Neg. Trop. Dis., 2019

📄 In silico methods for design of biological therapeutics. Methods, 2017

📄 Computational modeling of protein assemblies. Soni and Madhusudhan Curr. Opi. Str. Biol 2017

📄 High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy. Nucleic Acids Research (NAR), 2016

📄 Molecular Mechanism Underlying ATP-Induced Conformational Changes in the Nucleoprotein Filament of Mycobacterium smegmatis RecA, Biochemistry, 2016

📄 Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients, AIDS, 2014

📄 Biophysical properties of intrinsically disordered p130Cas substrate domain—implication in mechanosensing, PLOS Computational Biology, 2014

Manuscript in preparation

1. Dimerization preference of different Intermediate Filaments and molecular mechanisms of associated diseases. (In Preparation)

2. CLICK: A web server to mine structural databases for similar sub-structures of biological macromolecules and their complexes. (In preparation)

3. Disctransformation: A software to efficiently pack and score 3D objects in a given geometry. (In preparation)

4. GARLIC: A package for "Geometric Assessment of Residues using Locally Interacting Chemical groups". (In Preparation)

5. Evolution of Cooperation in Spatial Centipede Game. (In preparation)