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TERPRED: A Dynamic Structural Data Analysis Tool

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Recent Advances in Computer Science and Information Engineering

Part of the book series: Lecture Notes in Electrical Engineering ((LNEE,volume 125))

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Abstract

Computational protein structure prediction mainly involves the mainchain prediction and the side-chain confirmation determination. In this research, we developed a new structural bioinformatics tool, TERPRED for generating dynamic protein side-chain rotamer libraries. Compared with current various rotamer sampling methods, our work is unique in that it provides a method to generate a rotamer library dynamically based on small sequence fragments of a target protein. The Rotamer Generator provides a means for existing side-chain sampling methods using static pre-existing rotamer libraries, to sample from dynamic target-dependent libraries. Also, existing side-chain packing algorithms that require large rotamer libraries for optimal performance, could possibly utilize smaller, target-relevant libraries for improved speed.

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References

  1. Chou, P.Y., Fasman, G.D.: Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. Relat. Areas Molecular Biology 47, 45–148 (1978)

    Google Scholar 

  2. De Castro, E., Sigrist, C.J.A., Gattiker, A., Bulliard, V., Petra, S., Langendijk-Genevaux, P.S., Gasteiger, E., Bairoch, A., Hulo, N.: ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research 34, 362–365 (2006)

    Article  Google Scholar 

  3. Dunbrack, R.L.: Rotamer libraries in the 21st Century. Current Opinion Structural Biology 12(4), 431–440 (2002), doi:10.1016/S0959-440X(02)00344-5

    Article  Google Scholar 

  4. Lindahl, E., Elofsson, A.: Identification of related proteins on family, superfamily and fold level. J. Mol. Biol. 295(3), 613–625 (2000)

    Article  Google Scholar 

  5. Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Moecular Bioogyl. 247, 536–540 (1995)

    Google Scholar 

  6. Orengo, C.A., Michie, A.D., Jones, D.T., Swindells, M.B., Thornton, J.M.: CATH: A Hierarchic Classification of Protein Domain Structures. Structure 5, 1093–1108 (1997) ISSN: 0969-2126

    Article  Google Scholar 

  7. Peterson, R.W., Dutton, P.L., Wand, A.J.: Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library. Protein Sci. 13, 735–751 (2004)

    Article  Google Scholar 

  8. Xiang, Z., Honig, B.: Extending the accuracy limits of prediction for side-chain conformations. Journal of Molecular Biology 311, 421–430 (2001)

    Article  Google Scholar 

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Authors and Affiliations

  1. University of Arkansas at Little Rock, Little Rock, AR, 72204, USA

    Karl Walker & Steven F. Jennings

  2. Arkansas State University, AR, 72467, Jonesboro, USA

    Carole L. Cramer & Xiuzhen Huang

Authors
  1. Karl Walker
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  2. Carole L. Cramer
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  3. Steven F. Jennings
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  4. Xiuzhen Huang
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Corresponding author

Correspondence to Karl Walker .

Editor information

Editors and Affiliations

  1. , College of Communication Engineering, Jilin University, Room 313, Building No.1, Changchun, Nanhu Avenue 5372, Jilin, 130012, China, People's Republic

    Zhihong Qian

  2. , Department of Electrical Engineering, The University of Mississippi, Anderson Hall 314, Mississippi, 38677, Mississippi, USA

    Lei Cao

  3. , Department of Electrical and Computer En, Naval Postgraduate School, Rm. 452 Spanagel Bldg. 232, Dyer Road 833, Monterey, 93943-5121, California, USA

    Weilian Su

  4. , Faculty of Computing, London Metropolitan University, Holloway Road 166-220, London, N7 8DB, United Kingdom

    Tingkai Wang

  5. , College of Software, Changchun University of Science and Tech, Changchun, Jilin, 130022, China, People's Republic

    Huamin Yang

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© 2012 Springer-Verlag GmbH Berlin Heidelberg

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Walker, K., Cramer, C.L., Jennings, S.F., Huang, X. (2012). TERPRED: A Dynamic Structural Data Analysis Tool. In: Qian, Z., Cao, L., Su, W., Wang, T., Yang, H. (eds) Recent Advances in Computer Science and Information Engineering. Lecture Notes in Electrical Engineering, vol 125. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25789-6_106

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  • DOI: https://doi.org/10.1007/978-3-642-25789-6_106

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-25788-9

  • Online ISBN: 978-3-642-25789-6

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