J. S. Patel

Molecular modeling predicts novel antibody escape mutations in respiratory syncytial virus fusion glycoprotein

The paper uses molecular dynamics and FoldX to predict antibody escape mutations in RSV F protein and validates them experimentally.

Nuku, a family of primate retrogenes derived from KU70

The paper identifies and analyzes a family of primate retrogenes derived from KU70, showing evidence of functional divergence and positive selection in NUKU2.

EfgA is a conserved formaldehyde sensor that halts bacterial translation in response to elevated formaldehyde

This study identifies EfgA as a formaldehyde sensor in Methylorubrum extorquens that inhibits translation under formaldehyde stress, without enzymatic detoxification.

Implementing and assessing an alchemical method for calculating protein-protein binding free energy

The paper implements an alchemical method to calculate protein-protein binding free energy changes due to mutations and assesses its accuracy on small and large complexes.

Assessment of Software Methods for Estimating Protein-Protein Relative Binding Affinities

This study evaluates eight computational methods for predicting protein-protein relative binding affinities, finding some are accurate and efficient but less so for antibody-antigen complexes.

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

This study uses homology modeling and molecular dynamics simulations to predict the spectral peak of absorbance (λmax) for Sws2 cone photopigments with high accuracy.

Predicting the Viability of Beta-Lactamase: How Folding and Binding Free Energies Correlate with Beta-Lactamase Fitness

This paper evaluates how well thermodynamic folding and binding free energies predict the fitness of beta-lactamase mutants using experimental data and computational models.

Expanding the watch list for potential Ebola virus antibody escape mutations

This paper expands a watch list of potential Ebola virus antibody escape mutations by including three additional monoclonal antibodies and identifying 127 mutations, three of which have been observed in humans.