Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.

ABSTRACT: DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DN

SUBMITTER: Chakraborty D 

PROVIDER: S-EPMC10274755 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature