A. H. Elcock

AutoRNC: an automated modeling program for building atomic models of ribosome-nascent chain complexes

AutoRNC generates atomic models of ribosome-nascent chain complexes by sampling dipeptide conformations from RCSB, matching experimental data and enabling hypothesis generation for protein folding studies.

Modeling the 3D structure and conformational dynamics of very large RNAs using coarse-grained molecular simulations

This paper introduces a computational method to model and simulate the 3D structure and dynamics of large RNAs using coarse-grained molecular simulations and validates its accuracy against experimental data.

Multi-scale Modeling and Experimental Data Enable Structural Models of the Escherichia Coli Peptidoglycan to be Constructed on the Whole-Cell Scale

The paper constructs whole-cell scale structural models of E. coli peptidoglycan using computational modeling and experimental data, showing agreement with experimental pore size estimates and effects of lipoprotein distribution.

Atomic Models of All Major Trans-Envelope Complexes Involved in Lipid Trafficking in Escherichia Coli Constructed Using a Combination of AlphaFold2, AF2Complex, and Membrane Morphing Simulations

The paper constructs atomic models of four lipid transport TECs in E. coli using AlphaFold2, AF2Complex, and membrane morphing simulations.

Easy Removal of Steric Clashes and Entanglements in Macromolecular Systems by Temporary Addition of a Fourth Spatial Dimension

The paper introduces a method to resolve steric clashes and entanglements in macromolecular systems by temporarily adding a fourth spatial dimension and using potential functions to drive separation in 3D.

An Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides A Fast But Still Accurate Treatment Of Hydrodynamic Interactions In Brownian Dynamics Simulations Of Biological Macromolecules

This paper evaluates an orientationally averaged version of the Rotne-Prager-Yamakawa tensor for accelerating hydrodynamic interactions in Brownian dynamics simulations of biological macromolecules, showing high accuracy for translational diffusion but underestimation of rotational diffusion.