Computing and displaying intermolecular negative volume for docking

Mathematics and Visualization

Volumn 0, Issue 9783540260660, 2006, Pages 49-64

  Lee, Chang Ha ^a   Varshney, Amitabh ^a  

^a Institute of Advanced Computer Science   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS;

BIOCHEMICAL PROCESS; DESIGN CONSIDERATIONS; DOCKING SITES; GRAND CHALLENGE; GRAPHICS HARDWARE; INTERACTIVE 3D VISUALIZATIONS; PROTEIN DOCKING; SHAPE COMPLEMENTARITY;

THREE DIMENSIONAL COMPUTER GRAPHICS;

EID: 84979042576     PISSN: 16123786     EISSN: 2197666X     Source Type: Book Series    
DOI: 10.1007/3-540-30790-7_4     Document Type: Chapter

References (20)

1. M. L. Connolly. Solvent-accessible surfaces of proteins and nucleic acids. Science, 221:709-713, 1983.
2. M. L. Connolly. Shape complementarity at the hemoglobin a1b1 subunit interface. Biopolymers, 25:1229-1247, 1986.
3. G. Domik and G. Fels. HotDock: An interactive approach to molecular docking, 1996. http://www.uni-paderborn.de/lst/HotDock/.
4. H. Edelsbrunner, M. A. Facello, and J. Liang. On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics, 88(4):83-102, 1998.
5. H. Edelsbrunner, J. Liang, and C. Woodward. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science, 7(9):1884-1897, 1998.
6. R. Hawkes, S. Rushton, and M. Smyth. Update rates and fidelity in virtual environments. Virtual Reality: Research, Applications and Design, 1(2):46-51, 1995.
7. S. Jones and J. M. Thornton. Principles of protein—protein interactions. In Proc. Natl. Acad. Sci. USA, volume 93, pp. 13-20, 1996.
8. E. Katchalski-Katzir, I. Shariv, M. Eisenstein, A. A. Friesem, C. Aflalo, and I. A. Vakser. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. In Proceedings of the National Academy of Sciences of United States of America, volume 89, pp. 2195—2199, March 1992.
9. O. Kreylos, N. L. Max, B. Hamann, S. N. Crivelli, and E. W. Behel. Interactive protein manipulation. In Proceedings of the IEEE Visualization, pp. 581-588, Seattle, Washington, October 2003.
10. I. D. Kuntz. Structure-based strategies for drug design and discovery. Science, 257:1078— 1082, 1992.
11. R. A. Laskowski. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of Molecular Graphics, 13(5):323—330, 1995.
12. M. C. Lawrence and P. M. Colman. Shape complementarity at protein/protein interfaces. Journal of Molecular Biology, 234(4):946—950, 1993.
13. W. E. Lorensen and H. E. Cline. Marching cubes: a high resolution 3d surface construction algorithm. In Proceedings ofSIGGRAPH, pp. 163—169, July 1987.
14. K. Nadassy, I. Tomas-Oliveira, I. Alberts, J. Janin, and S. J. Wodak. Standard atomic volumes in double-stranded DNA and packing in protein—DNA interfaces. Nucleic Acids Research, 29(16):3362—3376, 2001.
15. A. Olson. Tangible interfaces for molecular biology. In Demos at the IEEE Visualization, page D12, Seattle, Washington, October 2003.
16. F. M. Richards. Areas, volumes, packing and protein structures. In Annual Review of Biophysics and Bioengineering, volume 6, pp. 151—176, 1977.
17. G. J. F. Smets and K. J. Overbeeke. Trade-off between resolution and interactivity in spatial task performance. IEEE Computer Graphics and Applications, 15(5):46—51, 1995.
18. A. Varshney, F. P. Brooks Jr., D. C. Richardson, W. V. Wright, and D. Manocha. Defining, computing, and visualizing molecular interfaces. In IEEE Visualization, pp. 36-43, October 1995.
19. E. A. Wintner and C. C. Moallemi. Quantized surface complementarity diversity (QSCD): A model based on small molecule-target complementarity. Journal of Medicinal Chemistry, 43:1993-2006, 2000.
20. J. M. Word, S. C. Lovell, T. H. LaBean, H. C. Taylor, M. E. Zalis, B. K. Presley, J. S. Richardson, and D. C. Richardson. Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms. Journal of Molecular Biology, 285(4):1711-1733, 1999.