Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes
Debayan Chakraborty1, Balaka Mondal1, D Thirumalai1,2
1Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA.
Biorxiv : the Preprint Server for Biology
|June 19, 2023
Summary
We developed COFFEE, a computational model for simulating DNA-protein complexes. This framework accurately predicts structural and dynamic properties, advancing our understanding of biophysical processes like gene expression.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- DNA-protein interactions are crucial for fundamental biological processes.
- Accurate computational models are needed to understand these interactions' structural and dynamic properties.
Conclusions:
- COFFEE is a robust and transferable framework for simulating DNA-protein complexes at the molecular length-scale.
- The model provides accurate predictions without force-field parameter readjustment.
- COFFEE offers a promising approach for studying complex molecular interactions in biology.
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