KIPS Transactions on Computer and Communication Systems (정보처리학회논문지:컴퓨터 및 통신 시스템)

Korea Information Processing Society (한국정보처리학회)
권호 표지
DOI QR코드

DOI QR Code

An Algorithm for Computing Valid Side Chain Conformations for Finding Transformed Channels in a Protein Molecule

단백질 분자에서 변형된 채널 발견을 위한 유효 사이드 체인 배치 알고리즘

  • Received : 2014.07.29
  • Accepted : 2014.10.30
  • Published : 2015.01.31
Download PDF
⟨ Previous Next ⟩

Abstract

This paper presents an algorithm for finding valid side chain conformations of amino acids, when given channel is transformed. The suggested algorithm implements a protein molecule with flexible side chains based on the flexibility of amino acids, and extracts adjacent amino acids that affect the formation of the channel. We detect the collision between adjacent amino acids and neighbors, in order to exclude invalid side chain conformations. Then, we construct the rotation angle combination tree to choose valid side chain conformations.

본 논문에서는 주어진 채널이 변형될 때, 아미노산들의 유효한 사이드 체인 배치(side chain conformation)를 찾는 알고리즘을 제시한다. 제안된 알고리즘은 아미노산의 유연성에 근거하여 사이드 체인 유연성을 가진 단백질 분자를 구현하고, 채널 변화에 영향을 주는 인접 아미노산(adjacent amino acid)을 추출한다. 인접 아미노산과 이웃(neighbor) 아미노산의 충돌 검사를 수행하여 유효하지 않은 사이드 체인 배치를 제거한 후, 회전각 조합 트리(rotation angle combination Tree)를 구성하여 사이드 체인 배치 중 유효한 것들만을 추출한다.

Keywords

References

  1. M. Petrek, P. Kosinova, J. Koca, and M. Otyepka, "MOLE: A Voronoi diagram-based explorer of molecular channels, Pores, and Tunnels," Structure, Vol.15, pp.1357-1363, 13 November, 2007. https://doi.org/10.1016/j.str.2007.10.007
  2. N. Lindow, D. Baum, and H.-C. Hege, "Voronoi-based extraction and visualization of molecular paths," IEEE Transaction on visualization and computer graphics, Vol.17, No.12, pp.2025-2034, December, 2011. https://doi.org/10.1109/TVCG.2011.259
  3. P. Medek, P. Benes, and J. Sochor, "Computation of tunnels in protein molecules using Delaunay triangulation," Journal of WSCG, Vol.15, pp.107-114, 2007.
  4. E. Chovancova, A. Pavelka, P. Benes, O. Strnad, J. Brezovsky, B. Kozlikova, A. Gora, V. Sustr, M. Klvana, P. Medek, L. Biedermannova, J. Sochor, and J. Damborsky, "CAVER 3.0 : A tool for the analysis of transport pathways in dynamic protein structures," PLOS Computational Biology, Vol.8, No.10, 2012.
  5. E. Yaffe, D. Fishelovitch, H. J. Wolfson, D. Halperin, and R. Nussinov, "MolAxis: Efficient and accurate identification of channels in macromolecules," Proteins: Structure, Function, and Bioinformatics, Vol.73, No.1, pp.72-86, 2008. https://doi.org/10.1002/prot.22052
  6. P. Benes, P. Medek, and J. Sochor, "Tracking single channel in protein dynamics," In WSCG Communication Papers proceedings, Vol.2, pp.109-114, 2010.
  7. B. J. Alder and T. E. Warinwright, "Studies in molecular dynamics," Journal of Chemical Physics, Vol.31, pp.459-466, Aug., 1959. https://doi.org/10.1063/1.1730376
  8. R. L. Dunbrack, "Rotamer libraries in the 21st century," Current Opinion in Structural Biology, Vol.12, pp.431-440, 2002. https://doi.org/10.1016/S0959-440X(02)00344-5
  9. B. Kim, J. E. Lee, Y. J. Kim, and K.-J. Kim, "GPU Accelerated Finding of Channels and Tunnels for a Protein Molecule," 11th IFIP International Conference on Network and Parallel Computing, September 8-20, Ilan, Taiwan (NPC 2014).