ArticlePloS one2009
Generating triangulated macromolecular surfaces by Euclidean Distance Transform.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- SHREC 2025: Protein surface shape retrieval including electrostatic potential.Computers & graphics · 2025Article
- Using AlphaFold and Symmetrical Docking to Predict Protein-Protein Interactions for Exploring Potential Crystallization Conditions.Proteins · 2025Article
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- Grid-Context Convolutional Model for Efficient Molecular Surface Construction from Point Clouds.Journal of chemical theory and computation · 2025Article
- Optimization of a sarbecovirus llama nanobody-antigen binding interface via a combined computational and phage display protein engineering approach.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2025Article
- PLO3S: Protein LOcal Surficial Similarity Screening.Computational and structural biotechnology journal · 2024Article
- sesA: A Program for the Analytic Computation of Solvent-Excluded Surface Areas.ChemistryOpen · 2024Article
- Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants.International journal of molecular sciences · 2024Article
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- Selectivity of Complex Coacervation in Multi-Protein Mixtures.bioRxiv : the preprint server for biology · 2024Article
- Structural Outlier Detection and Zernike-Canterakis Moments for Molecular Surface Meshes-Fast Implementation in Python.Molecules (Basel, Switzerland) · 2023Article
- Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds.The journal of physical chemistry letters · 2023Article
- EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations.Journal of molecular modeling · 2023Article
- Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds.Journal of cheminformatics · 2022Article
- 3β-Corner Stability by Comparative Molecular Dynamics Simulations.International journal of molecular sciences · 2022Article
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2 authors.
Funding
Abstract
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.
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