Marching cubes: A high resolution 3D surface construction algorithm
SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
Proceedings of the 18th annual conference on Computer graphics and interactive techniques
Fast generation of molecular surfaces from 3D data fields with an enhanced “marching cube” algorithm
Journal of Computational Chemistry
A Generalization of Algebraic Surface Drawing
ACM Transactions on Graphics (TOG)
CUDA accelerated blobby molecular surface generation
PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part I
Interactive exploration of protein cavities
EuroVis'11 Proceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization
Interactive extraction and tracking of biomolecular surface features
EuroVis '13 Proceedings of the 15th Eurographics Conference on Visualization
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Computing molecular surfaces is important to measure areas and volumes of molecules, as well as to infer useful information about interactions with other molecules. Over the years many algorithms have been developed to triangulate and to render molecular surfaces. However, triangulation algorithms usually are very expensive in terms of memory storage and time performance, and thus far from real-time performance. Fortunately, the massive computational power of the new generation of low-cost GPUs opens up an opportunity window to solve these problems: real-time performance and cheap computing commodities. This paper just presents a GPU-based algorithm to speed up the triangulation and rendering of molecular surfaces using CUDA. Our triangulation algorithm for molecular surfaces is based on a multi-threaded, parallel version of the Marching Cubes (MC) algorithm. However, the input of our algorithm is not the volume dataset of a given molecule as usual for Marching Cubes, but the atom centers provided by the PDB file of such a molecule. We also carry out a study that compares a serial version (CPU) and a parallel version (GPU) of the MC algorithm in triangulating molecular surfaces as a way to understand how real-time rendering of molecular surfaces can be achieved in the future.