Ronald M. Levy

This paper analyzes the binding of 50 type II inhibitors to 348 kinases, showing that protein reorganization significantly contributes to inhibitor selectivity with an AUC of ~0.8.

This paper benchmarks free energy calculations for protein mutations using two software platforms, showing strong correlations between predicted and experimental free energy changes.

This paper describes the engineering of high-affinity 3-phosphohistidine-specific antibodies using phage display and validates their utility in detecting pHis proteins in mammalian cells.

This paper introduces a method using molecular dynamics simulations to predict water positions in cryo-EM maps by analyzing excess chemical potential, showing high agreement with experimental data.

This study identifies the structural and sequence basis of epistatic interactions driving drug resistance in HIV by combining sequence models and molecular dynamics simulations.

This study evaluates ColabFold's ability to predict side chain conformations in proteins and shows how integrating it with a Potts model can explore mutation cooperativity.

The paper shows that protein evolution with epistasis and purifying selection does not lead to entrenchment, and that rate variation is due to epistasis, not historical contingency.

The paper investigates the structural basis for the distinct conformational landscapes of tyrosine and serine/threonine kinases using sequence and structure-based models.

The paper uses sequence coevolutionary analysis and structural contacts to reveal distinct residue interactions in GPCR classes A and B, providing insights for drug design.

The paper uses a Potts Hamiltonian model to infer epistatic effects in HIV-1 protease mutations, showing how these interactions influence drug resistance and fitness.