ArticleComputer methods in applied mechanics and engineering2009
A Fast Variational Method for the Construction of Resolution Adaptive C-Smooth Molecular Surfaces.
Article in Computer methods in applied mechanics and engineering, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Modeling regionalized volumetric differences in protein-ligand binding cavities.Proteome science · 2012Article
- Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy.Journal of structural biology · 2012Article
- A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids.Journal of chemical theory and computation · 2011Article
- AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS.SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics · 2011Article
- A dynamic data structure for flexible molecular maintenance and informatics.Bioinformatics (Oxford, England) · 2011Article
- Multi-domain, Higher Order Level Set Scheme for 3D Image Segmentation on the GPU.Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition · 2010Article
- F2Dock: fast Fourier protein-protein docking.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
3 authors.
Funding
Abstract
We present a variational approach to smooth molecular (proteins, nucleic acids) surface constructions, starting from atomic coordinates, as available from the protein and nucleic-acid data banks. Molecular dynamics (MD) simulations traditionally used in understanding protein and nucleic-acid folding processes, are based on molecular force fields, and require smooth models of these molecular surfaces. To accelerate MD simulations, a popular methodology is to employ coarse grained molecular models, which represent clusters of atoms with similar physical properties by psuedo- atoms, resulting in coarser resolution molecular surfaces. We consider generation of these mixed-resolution or adaptive molecular surfaces. Our approach starts from deriving a general form second order geometric partial differential equation in the level-set formulation, by minimizing a first order energy functional which additionally includes a regularization term to minimize the occurrence of chemically infeasible molecular surface pockets or tunnel-like artifacts. To achieve even higher computational efficiency, a fast cubic B-spline C(2) interpolation algorithm is also utilized. A narrow band, tri-cubic B-spline level-set method is then used to provide C(2) smooth and resolution adaptive molecular surfaces.
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