Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform

@article{Xu2013FastAA,
  title={Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform},
  author={Dong Xu and Hua Li and Yonghui Zhang},
  journal={Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB},
  year={2013},
  volume={7821},
  pages={
          304-316
        }
}
The depth of each atom/residue in a protein structure is a key attribution that has been widely used in protein structure modeling and function annotation. However, the accurate calculation of depth is time consuming. Here, we propose to use the Euclidean distance transform (EDT) to calculate the depth, which conveniently converts the protein structure to a 3D gray-scale image with each pixel labeling the minimum distance of the pixel to the surface of the molecule (i.e. the depth). We tested… CONTINUE READING
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