Ashar J. Malik

This study determines the crystal structure of AbTir, revealing how its coiled-coil domain inhibits NAD+ nucleosidase activity by disrupting symmetry and preventing NAD+ binding site formation.

The paper introduces a metric to quantify conformational noise in structural alphabets and shows its impact on phylogenetic inference using NMR ensembles and molecular dynamics simulations.

The paper introduces the Duplicate Monophyly Criterion to calibrate distance-matrix perturbations for phylogenetic support estimation using synthetic duplicates.

Structome-TM assembles datasets for structural phylogenetics by prioritizing local structural similarity to address size-based biases in homologous structure identification.

Structome-AlignViewer evaluates structure-aware alignments by mapping alignment columns to protein structures and providing confidence scores to identify reliable regions.

The paper introduces a quantum surrogate model framework for biophysical landscapes, demonstrating its ability to simulate transitions between localized and delocalized states using variational quantum eigensolver simulations.

The paper demonstrates a quantum-inspired kernel achieves high accuracy and Matthews correlation coefficient in classifying protein torsion angles, matching classical models.

The paper presents a dashboard for comparing and visualizing pathogenicity predictions of missense mutations in the human proteome within a 3D structural context.

The paper uses structure-based hidden Markov models to predict protein folds and infer function, particularly for proteins with weak sequence homology.

This paper uses tertiary-interaction characters to improve structural phylogenetics beyond the twilight zone, achieving accurate results with fast computation.

This paper explores encoding classical biomolecular data into quantum circuits for geometry optimization and uses quantum machine learning for protein side-chain classification.

Structome provides a web server to identify structural neighbors of proteins and generate datasets for structure-based phylogenetics using precomputed data.