A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances

@article{Dong2002ALA,
  title={A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances},
  author={Qunfeng Dong and Zhijun Wu},
  journal={J. Global Optimization},
  year={2002},
  volume={22},
  pages={365-375}
}
We describe a linear-time algorithm for solving the molecular distance geometry problem with exact distances between all pairs of atoms. This problem needs to be solved in every iteration of general distance geometry algorithms for protein modeling such as the EMBED algorithm by Crippen and Havel (Distance Geometry and Molecular Conformation, Wiley, 1988). However, previous approaches to the problem rely on decomposing an distance matrix or minimizing an error function and require O(n2) to O(n3… CONTINUE READING

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