Visualizing dynamic molecular conformations

Proceedings of the IEEE Visualization Conference

Volumn , Issue , 2002, Pages 235-242

  Schmidt Ehrenberg, Johannes ^a   Baum, Daniel ^a   Hege, Hans Christian ^a  

^a ZUSE INSTITUTE BERLIN   (Germany)

Author keywords

Drug design; Molecular conformation analysis; Molecular modeling; Uncertainty visualization

Indexed keywords

BIOCHEMISTRY; CONFORMATIONS; DRUG PRODUCTS; OPTIMIZATION; VISUALIZATION;

MOLECULAR CONFORMATIONS;

MOLECULAR GRAPHICS;

EID: 0036450525     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (18)

1. Amira ñ User's Guide and Reference Manual as well as Amira Programmer's Guide. Zuse Institute Berlin (ZIB) and Indeed - Visual Concepts GmbH, Berlin, http://www.amiravis.com, 2001.
2. AmiraMol ñ User's Guide and Reference Manual. Zuse Institute Berlin (ZIB) and Indeed - Visual Concepts GmbH, Berlin, http://www.amiravis.com, 2002.
3. Andrea Amadei, A.B.M. Linssen, and Herman J.C. Berendsen. Essential dynamics of proteins. Proteins: Structure, Function and Genomics, 17(4):412ñ425, 1993.
4. Jack E. Bresenham. Algorithm for computer control of digital plotter. IBM Syst. J., 4(1):25ñ30, 1965.
5. Daniel Cohen and Arie Kaufman. Scan-conversion algorithms for linear and quadratic objects. In Arie Kaufman, editor, Volume Visualization, pages 280ñ301. IEEE Computer Society Press, 1991.
6. Suzana Djurcilov, Kwansik Kim, Pierre F.J. Lermusiaux, and Alex Pang. Volume rendering data with uncertainty information. In D. Ebert, J.M. Favre, and R. Peikert, editors, Data Visualization 2001, Proceedings of the Joint EUROGRAPHICS - IEEE TCVG Symposium on Visualization. Springer-Verlag, Vienna, 2001.
7. Alexander Fischer, Christof Schütte, Peter Deu Hard, and Frank Cordes. Hierarchical uncoupling-coupling of metastable conformations. In Tamar Schlick and Hin Hark Gan, editors, Computational Methods for Macromolecules: Challenges and Applications, Proc. 3rd Int. Workshop on Algorithms for Macromolecular Modeling, New York, Oct. 2000, volume 24 of LNCSE, Berlin, 2002. Springer.
8. Tobias Galliat, Peter Deu Hard, Rainer Roitzsch, and Frank Cordes. Automatic identication of metastable conformations via self-organized neural networks. In T. Schlick and H.H. Gan, editors, Computational Methods for Macromolecules: Challenges and Applications - Proc. 3rd Int. Workshop on Algorithms for Macromolecular Modelling, volume 24 of LNCSE. Springer, 2002.
9. Henk Huitema and Robert van Liere. Interactive visualization of protein dynamics. In Proceedings of IEEE Vis2000, pages 465ñ468, October 2000.
10. Wolfgang Kabsch. A solution for the best rotation to relate two sets of vectors. Acta Crystallographica A, 32:922ñ923, 1976.
11. Wolfgang Kabsch. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallographiea A, 34:827ñ828, 1978.
12. Alex T. Pang, Craig M. Wittenbrink, and Suresh K. Lodha. Approaches to uncertainty visualization. The Visual Computer, 13(8):370ñ390, 1997.
13. Xavier Pennec. Multiple registration and mean rigid shape - Application to the 3D case. In K.V. Mardia, C.A. Gill, and Dryden I.L., editors, Image Fusion and Shape Variability Techniques (16th Leeds Annual Statistical Workshop), pages 178ñ185. University of Leeds, UK, July 1996.
14. Alexander Fischer Peter Den hard, Wilhelm Huisinga and Christof Schütte. Identi cation of almost invariant aggregates in reversible nearly uncoupled markov chains. Lin. Alg. Appl., 315:39ñ59, 2000.
15. Oliver Junge Peter Den hard, Michael Dellnitz and Christof Schütte. Computation of essential molecular dynamics by subdivision techniques. In P. Deu hard et.al., editor, Computational Molecular Dynamicsr: Challenges, Methods, Ideas, pages 98ñ115. Springer-Verlag, 1998. Lecture Notes in Computational Science an Engineering, Vol. 4.
16. Penny Rheingans and Shrikant Joshi. Visualization of molecules with positional uncertainty. In E. Gröller, H. Löffelmann, and W. Ribarsky, editors, Data Visualization '99, Proceedings of the Joint EUROGRAPHICS - IEEE TCVG Symposium on Visualization, pages 299ñ 306. Springer-Verlag, Vienna, 1999.
17. Christof Schütte. Conformational dynamics: Modelling, theory, algorithm, and application fo biomolecules. Habilitation Thesis, Dept. of Mathematics and Computer Science, Free University Berlin, 1998.
18. Maxim Totrov and Ruben Abagyan. The contour-buildup algorithm to calculate the analytical molecular surface. Journal of Structural Biology, 116:138ñ143, 1995.