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Shape Representation and Invariant Description of Protein Tertiary Structure in Applications to Shape Retrieval and Classification

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Advances in Geometric Modeling and Processing (GMP 2008)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4975))

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Abstract

Each protein tertiary structure is represented by three sorts of geometric models, which are polyline curves, triangulated surfaces and volumetric solids. Moment invariants are employed to describe the shapes of the three kinds of protein models and form a multidimensional feature vector for each model. We further analyze the influence of the three representations in applications to protein shape retrieval and classification.

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References

  1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Research 28, 235–242 (2000)

    Article  Google Scholar 

  2. Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: a Structural Classification of Proteins for the Investigation of Sequences and Structures. Journal of Molecular Biology 247, 536–540 (1995)

    Google Scholar 

  3. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., Thornton, J.M.: CATH- a Hierarchic Classification of Protein Domain Structures. Structure 5, 1093–1108 (1997)

    Article  Google Scholar 

  4. Holm, L., Ouzounis, C., Sander, C., Tuparev, G., Vriend, G.: A Database of Protein Structure Families with Common Folding Motifs. Protein Science 1, 1691–1698 (1992)

    Article  Google Scholar 

  5. Yeh, J.-S., Chen, D.-Y., Chen, B.-Y., Ouhyoung, M.: A Web-based Three-Dimensional Protein Retrieval System by Matching Visual Similarity. Bioinformatics 21, 3056–3057 (2005)

    Article  Google Scholar 

  6. Sanner, M.F., Olson, A.J., Spehner, J.-C.: Reduced Surface: An Efficient Way to Compute Molecular Surfaces. Biopolymers 38, 205–320 (1996)

    Article  Google Scholar 

  7. Chen, S.-C., Chen, T.: Protein Retrieval by Matching 3D Surfaces. In: Proceedings of the Workshop on Genomic Signal Processing and Statistics, vol. CP2-09, pp. 1–4 (2002)

    Google Scholar 

  8. Veltkamp, R.C., ter Haar, F.B.: SHREC, 3D Retrieval Contest. Technical Report UU-CS-2007-015 (2007)

    Google Scholar 

  9. Xu, D., Li, H.: Geometric Moment Invariants. Pattern Recognition 41, 240–249 (2008)

    Article  MATH  Google Scholar 

  10. Ankerst, M., Kastenmuller, G., Kriegel, H., Seidl, T.: Nearest Neighbor Classification in 3D Protein Databases. In: ISMB, pp. 34–43 (1999)

    Google Scholar 

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Falai Chen Bert Jüttler

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© 2008 Springer-Verlag Berlin Heidelberg

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Xu, D., Li, H., Gu, T. (2008). Shape Representation and Invariant Description of Protein Tertiary Structure in Applications to Shape Retrieval and Classification. In: Chen, F., Jüttler, B. (eds) Advances in Geometric Modeling and Processing. GMP 2008. Lecture Notes in Computer Science, vol 4975. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-79246-8_47

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  • DOI: https://doi.org/10.1007/978-3-540-79246-8_47

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-79245-1

  • Online ISBN: 978-3-540-79246-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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