ArticleResearch in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- )2013
Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform.
Article in Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Discriminating changes in protein structure using tyrosine conjugation.Protein science : a publication of the Protein Society · 2020Article
- iview: an interactive WebGL visualizer for protein-ligand complex.BMC bioinformatics · 2014Article
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3 authors.
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Abstract
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 the proposed EDT method on a set of 261 non-redundant protein structures. The data show that the EDT method is 2.6 times faster than the widely used method by Chakravarty and Varadarajan. The depth value by EDT method is also highly accurate, which is almost identical to the depth calculated by exhaustive search (Pearson's correlation coefficient≈1). We believe the EDT-based depth calculation program can be used as an efficient tool to assist the studies of protein fold recognition and structure-based function annotation.
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