Hi all,
I am planning to extend an enhanced sampling method, which has been successfully applied to protein-ligand systems, for use with protein-DNA complexes. One of the primary challenges in this endeavor is the computational cost. Therefore, I aim to initially test the method on systems as small as possible before applying it to larger, more complex systems.
For this purpose, I am considering two models:
1. SSO7D-DNA Complex (PDB: 1BBX), which consists of approximately 65 amino acids and serves as an example of non-specific protein-DNA binding.
2. Engrailed Homeodomain-DNA Complex (PDB: 1HDD), which contains around 60 amino acids and is an example of specific protein-DNA binding.
I am seeking suggestions or recommendations for other protein-DNA complexes with a smaller size than these. In particular, I would greatly appreciate complexes that have been extensively studied experimentally, with available data on binding affinity, association (kon), and dissociation (koff) rates, as these would be particularly valuable for validating the computational results.
Best regards,
Mohamed Marzouk Sobaih
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Received on Fri Sep 06 2024 - 16:30:02 PDT
