Geofold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability.

@article{Ramakrishnan2012GeofoldTP,
  title={Geofold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability.},
  author={Vibin Ramakrishnan and Sai Praveen Srinivasan and Saeed M. Salem and Suzanne J. Matthews and Wilfredo Col{\'o}n and Mohammed Zaki and Christopher Bystroff},
  journal={Proteins},
  year={2012},
  volume={80 3},
  pages={
          920-34
        }
}
Protein unfolding is modeled as an ensemble of pathways, where each step in each pathway is the addition of one topologically possible conformational degree of freedom. Starting with a known protein structure, GeoFold hierarchically partitions (cuts) the native structure into substructures using revolute joints and translations. The energy of each cut and its activation barrier are calculated using buried solvent accessible surface area, side chain entropy, hydrogen bonding, buried cavities… CONTINUE READING
6 Extracted Citations
53 Extracted References
Similar Papers

Referenced Papers

Publications referenced by this paper.
Showing 1-10 of 53 references

Similar Papers

Loading similar papers…