N. Ahalawat

Resolving Protein Conformational Plasticity and Substrate Binding Through the Lens of Machine-Learning

This paper uses machine learning to analyze molecular dynamics simulations of protein-ligand binding, identifying conformational states and allosteric sites involved in substrate recognition.

Reconciling Conformational Heterogeneity and Substrate Recognition in Cytochrome P450

This paper quantifies conformational heterogeneity in substrate-free cytochrome P450cam using simulations and identifies a dynamic equilibrium between closed and open conformations, suggesting an induced-fit mechanism for substrate recognition.

Non-affine displacements encode collective conformational fluctuations in proteins

The paper identifies non-affine displacements as key to resolving the free energy landscape of macromolecules using time-structured independent component analysis and Markov state models.

Mapping the Substrate Recognition Pathway in Cytochrome P450

This study uses molecular dynamics simulations to reveal the substrate recognition mechanism in cytochrome P450cam, showing that substrate entry occurs through a single channel without requiring large-scale loop opening.

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

The paper identifies collective displacements in apo-proteins that correlate with binding pathways without requiring actual binding events.

Assessment and Optimization of Collective Variables for Protein Conformational Landscape: GB1 β-hairpin as a Case Study

This paper identifies and optimizes collective variables to map the conformational landscape of GB1 β-hairpin, revealing four metastable states and a novel partial helical state.

Atomic Resolution Mechanism of Ligand Binding to a Solvent Inaccessible Cavity in T4 Lysozyme

This study uses molecular dynamics simulations to reveal the atomistic mechanism of benzene binding to a solvent-inaccessible cavity in L99A T4L, showing that subtle helix movements enable rapid ligand access without large conformational changes.