Paul C. Whitford

The paper uses a simulation model to show how ribosome structure and molecular sterics guide tmRNA translocation during trans-translation.

This study identifies bL27's role in preventing tmRNA from interfering with protein synthesis during trans-translation in bacteria.

The paper uses a structure-based model to study the asynchronous structural rearrangements during nuclear pore complex constriction and their energetic contributions.

The paper develops a theoretical model to study how ionic interactions influence subunit rotation in the yeast ribosome, showing that ion concentration changes significantly affect the energy landscape and kinetics of rotation.

The paper develops a multi-scale kinetic model and advanced assays to assess mRNA-LNP potency by integrating mechanistic understanding with multi-omics data.

The paper investigates the role of Mettl15 and Mettl17 in mitoribosome assembly, revealing their cooperative mechanism in transitioning from early to late stages of small subunit formation.

The paper identifies a novel antibiotic target site on the bacterial ribosome by showing how small molecules binding to ribosomal protein L33 can impede translation through steric obstruction.

This study identifies how RORγt mutations affect gene activation by altering chromatin binding modes, explaining context-dependent autoimmunity and host defense outcomes.

This study uses molecular simulations to show that subunit rotation in the ribosome non-monotonically affects tRNA kinetics, driven by steric contributions from a single ribosomal protein.

This study evaluates AlphaFold2's ability to predict peptide structural conformations using NMR data, finding varying accuracy with RMSD under 2.5 Å and RMSF under 1.5 Å.

The paper introduces the RAD method to quantitatively describe subunit rotations in ribosomes and applies it to analyze ribosome structures across organisms.

The paper introduces SMOG 2, a software package for designing and simulating structure-based biomolecular models using XML templates and PDB structures.