A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale

We present a general, robust, and efficient ray-casting-based approach to triangulating complex manifold surfaces arising in the nano-bioscience field. This feature is inserted in a more extended framework that: i) builds the molecular surface of nanometric systems according to several existing defi...

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Vydané v:PloS one Ročník 8; číslo 4; s. e59744
Hlavní autori: Decherchi, Sergio, Rocchia, Walter
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Public Library of Science 05.04.2013
Public Library of Science (PLoS)
Predmet:
Adenoviridae
Algorithms
Amidohydrolases - chemistry
Applied mathematics
Biology
Biophysics
Boltzmann equation
Boltzmann transport equation
Capsid - chemistry
Chemistry
Coloring
Computer Graphics
Computer Science
Fullerenes
Humans
Hydrogen
Manifolds
Materials Science
Mathematics
Models, Molecular
Nanotechnology
Physics
Poisson Distribution
Programming Languages
Protein Conformation
Reproducibility of Results
Robustness
Skin
Software packages
Solvents
Suites (Software)
Surface area
Surface Properties
Triangles
Viability
ISSN:1932-6203, 1932-6203
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Popis
Shrnutí:We present a general, robust, and efficient ray-casting-based approach to triangulating complex manifold surfaces arising in the nano-bioscience field. This feature is inserted in a more extended framework that: i) builds the molecular surface of nanometric systems according to several existing definitions, ii) can import external meshes, iii) performs accurate surface area estimation, iv) performs volume estimation, cavity detection, and conditional volume filling, and v) can color the points of a grid according to their locations with respect to the given surface. We implemented our methods in the publicly available NanoShaper software suite (www.electrostaticszone.eu). Robustness is achieved using the CGAL library and an ad hoc ray-casting technique. Our approach can deal with any manifold surface (including nonmolecular ones). Those explicitly treated here are the Connolly-Richards (SES), the Skin, and the Gaussian surfaces. Test results indicate that it is robust to rotation, scale, and atom displacement. This last aspect is evidenced by cavity detection of the highly symmetric structure of fullerene, which fails when attempted by MSMS and has problems in EDTSurf. In terms of timings, NanoShaper builds the Skin surface three times faster than the single threaded version in Lindow et al. on a 100,000 atoms protein and triangulates it at least ten times more rapidly than the Kruithof algorithm. NanoShaper was integrated with the DelPhi Poisson-Boltzmann equation solver. Its SES grid coloring outperformed the DelPhi counterpart. To test the viability of our method on large systems, we chose one of the biggest molecular structures in the Protein Data Bank, namely the 1VSZ entry, which corresponds to the human adenovirus (180,000 atoms after Hydrogen addition). We were able to triangulate the corresponding SES and Skin surfaces (6.2 and 7.0 million triangles, respectively, at a scale of 2 grids per Å) on a middle-range workstation.
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Conceived and designed the experiments: SD WR. Performed the experiments: SD. Analyzed the data: SD WR. Wrote the paper: SD WR.
Competing Interests: The authors have declared that no competing interests exist.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0059744