Shape modeling and matching in identifying protein structure from low-resolution images

Proceedings - SPM 2007: ACM Symposium on Solid and Physical Modeling

Volumn , Issue , 2007, Pages 223-232

  Abeysinghe, Sasakthi S ^a   Ju, Tao ^a   Chiu, Wah ^b   Baker, Matthew ^b  

^a WASHINGTON UNIVERSITY   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Cryo EM; Graph matching; Protein structure; Shape matching

Indexed keywords

GRAPH MATCHING; PROTEIN STRUCTURE; SHAPE MATCHING;

GRAPH THEORY; HEURISTIC ALGORITHMS; IMAGE ANALYSIS; THREE DIMENSIONAL;

PROTEINS;

EID: 35348865170     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1236246.1236278     Document Type: Conference Paper

References (46)

1. BAKER, M., JU, T., AND CHIU, W. 2007. Identification of secondary structure elements in intermediate resolution density maps. Structure 15, 7-19.
2. BALDI, P., BRUNAK, S., FRASCONI, P., SODA, G., AND POLLASTRI, G. 1999. Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15, 937.
3. BERTRAND, G. 1995. A parallel thinning algorithm for medial surfaces. Pattern Recogn. Lett. 16, 9, 979-986.
4. BORGEFORS, G., NYSTRÖM, I., AND SANNITI DI BAJA, G. 1999. Computing skeletons in three dimensions. Pattern Recognition 32, 7, 1225-1236.
5. BUNKE, H., AND ALLERMANN, G. 1983. Inexact graph matching for structural pattern recognition. Pattern Recognition Letters 1, 245-253.
6. BUNKE, H., AND MESSMER, B. T. 1997. Recent advances in graph matching. IJPRAI 11, 1, 169-203.
7. BUNKE, H. 1999. Error correcting graph matching: On the influence of the underlying cost function. IEEE Trans. Pattern Anal. Mach. Intell. 21, 917-922.
8. CHEN, D., TIAN, X., SHEN, Y., AND OUHYOUNG, M. 2003. On visual similarity based 3d model retrieval. Computer Graphics Forum 22, 3, 223-232. Eurographics 2003 Conference Proceedings.
9. CHIU, W., BAKER, M., JIANG, W., DOUGHERTY, M., AND SCHMID, M. 2005. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure (Comb) 13, 363-372.
10. CHRISTMAS, W. J., KITTLER, J., AND PETROU, M. 1995. Structural matching in computer vision using probabilistic relaxation. IEEE Trans. Pattern Anal. Mach. Intell. 17, 8, 749-764.
11. CONTE, D., FOGGIA, P., SANSONE, C., AND VENTO, M. 2004. Thirty years of graph matching in pattern recognition. International Journal of Pattern Recognition and Artificial Intelligence.
12. CORDELLA, L. P., FOGGIA, P., SANSONE, C., AND VENTO, M. 1999. Performance evaluation of the vf graph matching algorithm. In International Conference on Image Analysis and Processing.
13. DUTTA, S., AND BERMAN, H. 2005. Large macromolecular complexes in the protein data bank: a status report. Structure 13, 381-388.
14. FENG, J., LAUMY, M., AND DHOME, M. 1994. Inexact matching using neural networks. Pattern Recognition in Practice IV: Multiple Paradigms, Comparative Studies, and Hybrid Systems, 177-184.
15. FUNKHOUSER, T., AND SHILANE, P. 2006. Partial matching of 3D shapes with priority-driven search. In Symposium on Geometry Processing.
16. GAL, R., AND COHEN-OR, D. 2006. Salient geometric features for partial shape matching and similarity. ACM Trans. Graph. 25, 1, 130-150.
17. GATZKE, T., ZELINKA, S., GRIMM, C., AND GARLAND, M. 2005. Curvature maps for local shape comparison. In Shape Modeling International, 244-256. A local shape comparison technique for meshes.
18. HERAULT, L., HORAUD, R., VEILLON, F., AND NIEZ, J. J. 1990. Symbolic image matching by simulated annealing. In Proc. British Machine Vision Conference (BMVC90), 319-324.
19. HORAUD, R., AND SKORDAS, T. 1989. Stereo correspondence through feature grouping and maximal cliques. IEEE Trans. Pattern Anal. Mach. Intell. 11, 11, 1168-1180.
20. JIANG, W., BAKER, M., LUDTKE, S., AND CHIU, W. 2001. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J Mol Biol 308, 1033-1044.
21. JU, T., BAKER, M., AND CHIU, W. 2006. Computing a family of skeletons of volumetric models for shape description. In Geometric Modeling and Processing, 235-247.
22. LOWE, D. G. 2004. Distinctive image features from scale-invariant keypoints. International Journal of Computer Vision 60, 2, 91-110.
23. MESSMER, B. T., AND BUNKE, H. 1998. A new algorithm for error-tolerant subgraph isomorphism detection. IEEE Trans. Pattern Anal. Mack Intell. 20, 5, 493-504.
24. MOULT, J. 2005. A decade of casp: progress, bottlenecks and prognosis in protein structure prediction. Current Opinion in Structural Biology 15, 285-289.
25. NILSSON, N. 1980. Principles of Artificial Intelligence. Morgan Kaufmann Publishers.
26. PALÁGYI, K., AND KUBA, A. 1999. A parallel 3d 12-subiteration thinning algorithm. Graph. Models Image Process. 61, 4, 199-221.
27. PENCZEK, P. A., GRASSUCCI, R. A., AND FRANK, J. 1994. The ribosome at improved resolution: New techniques for merging and orientation refinement in 3d cryo-electron microscopy of biological particles. Ultramicroscopy 53, 3, 251-270.
28. ROHL, C., STRAUSS, C., MISURA, K., AND BAKER, D. 2005. Protein structure prediction using rosetta. Methods Enzymol 383, 66-93.
29. SALI, A., AND OVERINGTON, J. 1994. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 3, 1582-1596.
30. SALI, A. 1998. 100,000 protein structures for the biologist. Nat Struct Biol 5, 1029-1032.
31. SANFELIU, A., AND FU, K. 1983. A distance measure between attributed relational graphs for pattern recognition. IEEE Trans. Systems, Man, and Cybernetics 13, 353-363.
32. SHAPIRO, L. G., AND HARALICK, R. M. 1981. Structural descriptions and inexact matching. IEEE Trans. Pattern Anal. Mach. Intell. 5, 5, 504-519.
33. SHEN, M., AND SALI, A. 2006. Statistical potential for assessment and prediction of protein structures. Protein Sci. 15, 11, 2507-2524.
34. SHILANE, P., MIN, P., KAZHDAN, M., AND FUNKHOUSER, T. 2004. The princeton shape benchmark. In SMI '04: Proceedings of the Shape Modeling International 2004 (SMI'04), IEEE Computer Society, Washington, DC, USA, 167-178.
35. SIPPL, M. J. 1993. Boltzmann's principle, knowledge-based mean fields and protein folding, an approach to the computational determination of protein structures. J Comput Aided Mol Des 7, 4, 473-501.
36. SIPPL, M. J. 1999. Who solved the protein folding problem? Structure 7, 4, R81-R83.
37. SUNDAR, H., SILVER, D., GAGVANI, N., AND DICKINSON, S. J. 2003. Skeleton based shape matching and retrieval. In Shape Modeling International, 130-142, 290.
38. SVENSSON, S., NYSTRÖM, I., AND SANNITI DI BAJA, G. 2002. Curve skeletonization of surface-like objects in 3d images guided by voxel classification. Pattern Recognition Letters 23, 12 (October), 1419-1426.
39. TSAI, W. H., AND FU, K. S. 1979. Error-correcting isomorphisms of attributed relational graphs for pattern recognition. IEEE Trans. Systems, Man, and Cybernetics 9, 757-768.
40. ULLMANN, J. R. 1976. An algorithm for subgraph isomorphism. J. ACM 23, 1, 31-42.
41. VENCLOVAS, C., AND MARGELEVICIUS, M. 2005. Comparative modeling in casp6 using consensus approach to template selection, sequence-structure alignment, and structure assessment. Proteins: Structure, Function, and Bioinformatics 61, S7, 99-105.
42. WANG, Y., FAN, K., AND HORNG, J. 1997. Genetic-based search for error-correcting graph isomorphism. IEEE Transactions on Systems, Man, and Cybernetics, Part B 27, 4, 588-597.
43. WONG, A., YOU, M., AND CHAN, A. 1990. An algorithm for graph optimal monomorphism. IEEE Trans. Systems, Man, and Cybernetics 20, 3, 628-636.
44. WU, Y., CHEN, M., LU, M., WANG, Q., AND MA, J. 2005. Determining protein topology from skeletons of secondary structures. J. Mol. Biol., 350, 3, 571-586.
45. ZHANG, Y., AND SKOLNICK, J. 2005. The protein structure prediction problem could be solved using the current pdb library. Proc Natl Acad Sci USA 102, 4, 1029-1034.
46. ZHANG, J., SIDDIQI, K., MACRINI, D., SHOKOUFANDEH, A., AND DICKINSON, S. J. 2005. Retrieving articulated 3-d models using medial surfaces and their graph spectra. In EMMCVPR, 285-300.