Yash Bhargava

Retrieval of binding sites across the AlphaFold human proteome using protein language model representations

PocketScope retrieves binding sites across the AlphaFold human proteome using protein language model representations and achieves top performance on a benchmark.

In Silico Targeting of Calpain-5 in Autosomal Dominant Neovascular Inflammatory Vitreoretinopathy (ADNIV) with Peptides and Natural Products

This paper identifies druggable pockets of CAPN5 and screens natural products and peptides to find inhibitors for ADNIV.

NDST1 as a substrate-reduction target in Mucopolysaccharidosis type IIIC: virtual screening, microsecond molecular dynamics, and peptide design

The paper identifies small-molecule and peptide inhibitors of NDST1 as potential substrate-reduction therapies for MPS IIIC using computational screening and molecular dynamics.

Dynamics of the α2-chimaerin-Rac1 interface in Duane retraction syndrome and computational design of candidate probes

The paper characterizes the dynamics of the CHN1-Rac1 interface in Duane retraction syndrome and identifies candidate chemical probes using computational methods.

A Chromatin Biology Assessment of AlphaFold3

This paper benchmarks AlphaFold3's ability to predict structures of chromatin complexes, finding it excels at histone interactions but struggles with DNA-binding factors.

Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with {lambda}-dynamics

This paper uses {lambda}-dynamics to predict RNA binding preferences of human Pumilio, including modified RNAs, showing high accuracy compared to experimental data.