Exploring cavity dynamics in biomolecular systems

BMC Bioinformatics

Volumn 14, Issue 19, 2013, Pages

  Lindow, Norbert ^a   Baum, Daniel ^a   Bondar, Ana Nicoleta ^b   Hege, Hans Christian ^a  

^a ZUSE INSTITUTE BERLIN   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; VAN DER WAALS FORCES;

ACCURATE COMPUTATIONS; CONFORMATIONAL CHANGE; MOLECULAR DYNAMICS TRAJECTORIES; PRE-PROCESSING STEP; RAPID IDENTIFICATION; TIME-DEPENDENT CHANGES; TIME-DEPENDENT DYNAMICS; TIME-DEPENDENT STRUCTURE;

PROTEINS;

BACTERIORHODOPSIN; PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER GRAPHICS; METHODOLOGY; MOLECULAR DYNAMICS; PROTEIN CONFORMATION;

ALGORITHMS; BACTERIORHODOPSINS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS;

EID: 84899908873     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S19-S5     Document Type: Article

References (27)

1. Dror RO, Jensen M, Borhani DW, Shaw DE: Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J Gen Physiol. 2010, 135 (6): 555-562. 10.1085/jgp.200910373. [ http://dx.doi.org/10.1085/jgp.200910373 ]
2. Lindow N, Baum D, Hege HC: Voronoi-Based Extraction and Visualization of Molecular Paths. IEEE Trans Vis Comput Graphics. 2011, 17 (12): 2025-2034.
3. Lindow N, Baum D, Bondar AN, Hege HC: Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization. Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12). 2012
4. Herzfeld J, Lansing J: Magnetic resonance studies of the bacteriorhodopsin pump cycle. Annu Rev Biophys Biomol Struct. 2002, 31:
5. Kouyama T, Nishikawa T, Tokuhisa T, Okumura H: Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle. Journal of Molecular Biology. 2004, 335 (2): 531-546. 10.1016/j.jmb.2003.10.068.
6. Smart OS, Neduvelil JG, Wang X, Wallace BA: HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph. 1996, 14 (6): [ http://view.ncbi.nlm.nih.gov/pubmed/9195488 ]
7. Ho BK, Gruswitz F: HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct Biol. 2008, 8: 49+-10.1186/1472-6807-8-49. [ http://dx.doi.org/10.1186/1472-6807-8-49 ]
8. Parulek J, Turkay C, Reuter N, Viola I: Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations. Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12). 2012
9. Petrěk M, Otyepka M, Banas P, Kosinová P: CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics. 2006, 7: 316+-10.1186/1471-2105-7-316. [ http://dx.doi.org/10.1186/1471-2105-7-316 ]
10. Petrěk M, Kosinová P, Koca J, Otyepka M: MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure. 2007, 15 (11): 1357-1363. 10.1016/j.str.2007.10.007. [ http://www.sciencedirect.com/science/article/B6VSR-4R46KGV-8/2/b0b51ca7cbaa1dbcbc15b3c9fd7fd0cb ]
11. Medek P, Beneš P, Sochor J: Computation of tunnels in protein molecules using Delaunay triangulation. J of WSCG. 2007, 15 (1-3): 107-114.
12. Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R: MolAxis: Efficient and accurate identification of channels in macromolecules. Proteins: Struct, Funct, Bioinf. 2008, 73: 72-86. 10.1002/prot.22052. [ http://dx.doi.org/10.1002/prot.22052 ]
13. Raunest M, Kandt C: dxTuber: Detecting Protein Cavities, Tunnels and Clefts Based on Protein and Solvent Dynamics. J Mol Graph Model. 2010
14. Krone M, Grottel S, Ertl T: Parallel Contour-Buildup Algorithm for the Molecular Surface. Proc IEEE Symposium on Biological Data Visualization (BioVis 2011). 2011, 17-22.
15. Kim DS, Cho Y, Kim D: Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Comput Aided Des. 2005, 37 (13): 1412-1424. 10.1016/j.cad.2005.02.013.
16. Gibson K, Scheraga H: Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii. Molecular Physics. 1987, 62 (5): 1247-1265. 10.1080/00268978700102951.
17. Petitjean M: On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects. Journal of Computational Chemistry. 1994, 15 (5): 507-523. 10.1002/jcc.540150504.
18. OpenCL Website. 2012, [ http://www.khronos.org/opencl/ ]
19. Lindow N, Baum D, Prohaska S, Hege HC: Accelerated Visualization of Dynamic Molecular Surfaces. Comput Graph Forum. 2010, 29 (3): 943-952. 10.1111/j.1467-8659.2009.01693.x. [ http://dx.doi.org/10.1111/j.1467-8659.2009.01693.x ]
20. Edelsbrunner H: Deformable Smooth Surface Design. Discrete Comput Geom. 1999, 21: 87-115. 10.1007/PL00009412.
21. Grigoryan G, Rheingans P: Point-Based Probabilistic Surfaces to Show Surface Uncertainty. IEEE Transactions on Visualization and Computer Graphics. 2004, 10 (5): 564-573. 10.1109/TVCG.2004.30. [ http://dx.doi.org/10.1109/TVCG.2004.30 ]
22. Pöthkow K, Weber B, Hege HC: Probabilistic Marching Cubes. Computer Graphics Forum. 2011, 30 (3): 931-940. 10.1111/j.1467-8659.2011.01942.x. [ http://www.zib.de/visual/publications/sources/src-2011/probabilistic_marching_cubes.pdf ]
23. Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK: Structure of bacteriorhodopsin at 1.55 Åresolution. J Mol Biol. 1999, 291 (4): 899-911. 10.1006/jmbi.1999.3027. [ http://www.sciencedirect.com/science/article/pii/S0022283699930279 ]
24. Grudinin S, Büldt G, Gordeliy V, Baumgaertner A: Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin - Molecular Dynamics Simulations of the Ground State and the M-Intermediate. Biophys J. 2005, 88 (5): 3252-3261. 10.1529/biophysj.104.047993. [ http://www.sciencedirect.com/science/article/pii/S0006349505733762 ]
25. Bondar AN, Fischer S, Smith J: Water Pathways in the Bacteriorhodopsin Proton Pump. J Membr Biol. 2011, 239: 73-84. 10.1007/s00232-010-9329-3. [10.1007/s00232-010-9329-3], [ http://dx.doi.org/10.1007/s00232-010-9329-3 ]
26. Krone M, Falk M, Rehm S, Pleiss J, Ertl T: Interactive Exploration of Protein Cavities. Comput Graph Forum. 2011, 30 (3): 673-682. 10.1111/j.1467-8659.2011.01916.x.
27. Meyer-Spradow J, Ropinski T, Vahrenhold J, Hinrichs K: K.H.: Illustrating Dynamics of Time-Varying Volume Datasets in Static Images. In: Proceedings of Vision, Modeling and Visualization 2006. 2006, 333-340.