ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison.

ABSTRACT: Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from nanoscale nonrandom machine-like motions induced by evolutionarily conserved molecular interactions. Comparisons of molecular dynamics (MD) simulations conducted between homologous sites representative of different functional or mutational states can potentially identify local effects on binding interaction and protein evolution. In addition, comparisons of different (i.e., nonhomologous) sites within MD simulations could be employed to identify functional shifts in local time-coordinated dynamics indicative of logic gating within proteins. However

SUBMITTER: Babbitt GA 

PROVIDER: S-EPMC11393699 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature