A. K. Padhi

Hotspot residues and resistance mutations in the nirmatrelvir-binding site of SARS-CoV-2 main protease: Design, identification, and correlation with globally circulating viral genomes

The paper identifies hotspot residues and resistance mutations in SARS-CoV-2 Mpro using protein design and correlates them with global viral genomes.

Scanning the RBD-ACE2 molecular interactions in Omicron variant

This study uses molecular dynamics simulations to compare the RBD-ACE2 interactions between the SARS-CoV-2 wild-type and Omicron variants, revealing changes in charge, dynamics, and energetics.

Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOCs)

This study analyzes the molecular dynamics of SARS-CoV-2 variants of concern using simulations, finding differences in binding energy and electrostatic interactions compared to the wild-type.

Seven amino acid types suffice to reconstruct the core fold of RNA polymerase

The paper reconstructs the DPBB fold using only seven amino acid types, suggesting it could have emerged with the early genetic code.

High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19

The paper uses high-throughput computation to design and map mutations in the RBD-ACE2 interface of SARS-CoV-2, identifying affinity-enhancing and weakening mutations that impact infectivity and pathogenesis.