Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

By Dong Xu, Yang Zhang. 2009

136 citations recorded by the source corpus.

Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT). The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2–4% depending on the grid resolution, which is 1.5–4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf.

Subfields: Computational Theory and Mathematics, Computer Graphics and Computer-Aided Design, Computer Vision and Pattern Recognition

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Citations in the corpus

Toward optimal fragment generations for ab initio protein structure assembly (2012, methodology): “The solvent accessibility for template structures is calculated by EDTSurf, 34 which generates triangulated solvent-accessible surface using the fast Euclidean distance transform technique, where the solvent accessibility of each residue is defined as the ratio of the accessible surface area in prot”
Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field (2012, background): “35 However, the calculation can be time consuming.”
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds (2020, methodology): “Next, the EDTSurf method[4,5] is used to voxelize cartesian space at 0.”
Finding correct protein–protein docking models using ProQDock (2016, unknown): “First, the molecular surface (Connolly, 1983) was generated individually for both the partner molecules using the software EDTSurf (Xu and Zhang, 2009), with the scale factor for the optimum fit of the molecule in a bounding box set to 1.”
FreeSASA: An open source C library for solvent accessible surface area calculations (2016, background): “The surface area can also be calculated analytically (Fraczkiewicz and Braun, 1998), which is useful when the gradient is needed, or by various other approximations, tailored for different purposes (Sanner et al., 1996; Weiser et al., 1999; Cavallo et al., 2003; Xu and Zhang, 2009; Drechsel et al., ”
The RCSB Protein Data Bank: new resources for research and education (2012, methodology): “Surfaces are created for all macromolecule chains in a PDB entry using the Euclidean distance transform algorithm from Xu and Zhang (39).”