A basin hopping algorithm for protein-protein docking

@article{Hashmi2012ABH,
  title={A basin hopping algorithm for protein-protein docking},
  author={Irina Hashmi and Amarda Shehu},
  journal={2012 IEEE International Conference on Bioinformatics and Biomedicine},
  year={2012},
  pages={1-4}
}
We present a novel probabilistic search algorithm to efficiently search the structure space of protein dimers. The algorithm is based on the basin hopping framework that repeatedly follows up structural perturbation with energy minimization to obtain a coarse-grained view of the dimeric energy surface in terms of its local minima. A Metropolis criterion biases the search towards lower-energy minima over time. Extensive analysis highlights efficient and effective implementations for the… CONTINUE READING

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