## Visualizing Dynamic Molecular Conformations (2002)

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### Other Repositories/Bibliography

Venue: | Proceedings of IEEE Visualization 2002 |

Citations: | 7 - 2 self |

### BibTeX

@INPROCEEDINGS{Schmidt-ehrenberg02visualizingdynamic,

author = {Johannes Schmidt-ehrenberg and Daniel Baum and Hans-christian Hege},

title = {Visualizing Dynamic Molecular Conformations},

booktitle = {Proceedings of IEEE Visualization 2002},

year = {2002},

pages = {235--242},

publisher = {IEEE Computer Society, IEEE Computer Society Press}

}

### OpenURL

### Abstract

The bioactivity of a molecule strongly depends on its metastable conformational shapes and the transitions between these. Therefore, conformation analysis and visualization is a basic prerequisite for the understanding of biochemical processes.

### Citations

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Citation Context ...tives, cylinders and spheres, we use an algorithm as proposed by Cohen and Kaufman in [5]. Scan-converting a cylinder is done by first applying an extension of the 2-dimensional Bresenham’s algorith=-=m [4] to -=-three dimensions to compute a voxelization of the cylinder’s center line. Second, we rasterize one slice of the cylinder, i.e. a circle, and move this slice to each voxel of the cylinder’s center ... |

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Citation Context ...al task in molecular science. When two molecules are to be compared based on Cartesian atom coordinates, alignment is necessary to eliminate differences caused by global rigid transformations. Kabsch =-=[10, 11]-=- gives a straight forward method to compute an alignment between two point sets. Pennec [13] develops an approach to align multiple point sets iteratively. Both methods are characterized in more detai... |

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Citation Context ...ncept of essential dynamics [3]. They interpret the dynamics of a protein as a trajectory in a high dimensional space and employ covariance analysis to filter out large concerted motions. Pang et al. =-=[12]-=- developed various techniques for presenting data together with uncertainty and presented a classification of the possibilities of uncertainty visualization. Djurcilov et al. [6] proposed two methods ... |

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Citation Context ...h methods are characterized in more detail in Section 4.1. Huitema and van Liere [9] describe techniques for interactive visualization of protein dynamics, utilizing the concept of essential dynamics =-=[3]-=-. They interpret the dynamics of a protein as a trajectory in a high dimensional space and employ covariance analysis to filter out large concerted motions. Pang et al. [12] developed various techniqu... |

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Citation Context ...additional bit field to keep track of those nodes already counted. For the rasterization of the two kinds of primitives, cylinders and spheres, we use an algorithm as proposed by Cohen and Kaufman in =-=[5]. Sc-=-an-converting a cylinder is done by first applying an extension of the 2-dimensional Bresenham’s algorithm [4] to three dimensions to compute a voxelization of the cylinder’s center line. Second, ... |

28 |
Conformational Dynamics: Modelling, Theory, Algorithm, and Applications to Biomolecules
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Citation Context ...ble conformation of the molecule, and classify the molecular geometries qi into these sets. To accomplish that, a novel approach on the basis of a transfer operator has been employed; for details see =-=[15, 17, 14, 8]-=-. Isosurface 4 VISUALIZATION OF MOLECULAR CONFORMATIONS In the following section we will describe techniques for the visualization of molecular metastable conformations. Before we go into detail, we w... |

14 |
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Citation Context ... we also implemented an algorithm for the generation of a triangular representation of the solvent excluded, solvent accessible, and the van der Waals surface, based on the work of Totrov and Abagyan =-=[18]-=-. To address the problem of conformation visualization in Amira we represent discrete samplings of conformational densities as pseudo time series where every sample geometry is a time step. The geomet... |

13 | Multiple registration and mean rigid shape - application to the 3D case
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Citation Context ...dinates, alignment is necessary to eliminate differences caused by global rigid transformations. Kabsch [10, 11] gives a straight forward method to compute an alignment between two point sets. Pennec =-=[13]-=- develops an approach to align multiple point sets iteratively. Both methods are characterized in more detail in Section 4.1. Huitema and van Liere [9] describe techniques for interactive visualizatio... |

12 | Volume rendering data with uncertainty information
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(Show Context)
Citation Context ...motions. Pang et al. [12] developed various techniques for presenting data together with uncertainty and presented a classification of the possibilities of uncertainty visualization. Djurcilov et al. =-=[6]-=- proposed two methods for incorporating volumetric uncertainty information in direct volume rendering. Techniques for visualizing molecules with positional uncertainty are discussed by Rheingans and J... |

11 | Visualization of molecules with positional uncertainty
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Citation Context ...osed two methods for incorporating volumetric uncertainty information in direct volume rendering. Techniques for visualizing molecules with positional uncertainty are discussed by Rheingans and Joshi =-=[16]-=-. They developed a likelihood volume representation where for a given set of molecules a Gaussian splat is drawn for each atom of each molecule. The resultant scalar field is depicted either by iso-su... |

8 | LIERE R.: Interactive visualization of protein dynamics
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(Show Context)
Citation Context ...ute an alignment between two point sets. Pennec [13] develops an approach to align multiple point sets iteratively. Both methods are characterized in more detail in Section 4.1. Huitema and van Liere =-=[9]-=- describe techniques for interactive visualization of protein dynamics, utilizing the concept of essential dynamics [3]. They interpret the dynamics of a protein as a trajectory in a high dimensional ... |

4 | Hierarchical uncoupling–coupling of metastable conformations
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Citation Context ...states xi (i = 1, ..., Mtot) are distributed according to the density fcan. The Hybrid Monte Carlo technique employed for generation of the molecular configurations used in this paper is described in =-=[7]. 3.-=-3 Conformation Analysis The phrase ‘metastable conformation’ indicates a dynamic aspect of molecular behavior: it denotes metastable shapes, i.e. molecular geometries which survive the fast oscill... |

3 |
Schutte C: Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains
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(Show Context)
Citation Context ...ble conformation of the molecule, and classify the molecular geometries qi into these sets. To accomplish that, a novel approach on the basis of a transfer operator has been employed; for details see =-=[15, 17, 14, 8]-=-. Isosurface 4 VISUALIZATION OF MOLECULAR CONFORMATIONS In the following section we will describe techniques for the visualization of molecular metastable conformations. Before we go into detail, we w... |

2 |
Identification of metastable conformations via self-organized neural networks
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(Show Context)
Citation Context ...ble conformation of the molecule, and classify the molecular geometries qi into these sets. To accomplish that, a novel approach on the basis of a transfer operator has been employed; for details see =-=[15, 17, 14, 8]-=-. Isosurface 4 VISUALIZATION OF MOLECULAR CONFORMATIONS In the following section we will describe techniques for the visualization of molecular metastable conformations. Before we go into detail, we w... |

2 |
The contour-buildup algorithm to calculate the analytical molecular surface
- Totorov, Abagyan
- 1996
(Show Context)
Citation Context ... we also implemented an algorithm for the generation of a triangular representation of the solvent excluded, solvent accessible, and the van der Waals surface, based on the work of Totrov and Abagyan =-=[18]-=-. To address the problem of conformation visualization in Amira we represent discrete samplings of conformational densities as pseudo time series where every sample geometry is a time step. The geomet... |