KIPS Transactions on Software and Data Engineering (정보처리학회논문지:소프트웨어 및 데이터공학)

Korea Information Processing Society (한국정보처리학회)
권호 표지
DOI QR코드

DOI QR Code

Three Dimensional Visualization of Contact Region for a Protein Complex

단백질 복합체를 위한 접촉 영역의 3차원 가시화

  • 강범식 (경북대학교 생명과학부) ;
  • 김구진 (경북대학교 컴퓨터학부) ;
  • 김유경 (경북대학교 대학원 컴퓨터학부)
  • Received : 2013.08.19
  • Accepted : 2013.10.17
  • Published : 2013.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

In this paper, we present a method to visualize the contact region between two molecules in a protein complex in a threedimensional space. The contact region of two molecules shows compatibility in geometric aspects. Usually, the computation of the area of contact region has been used to show the strength of compatibility. The numerical value and simple drawing of contact region would be useful for comparing the relative strength of different contacts, but it is not appropriate for analysing the geometric characteristics of the contact region. In this paper, we present a method to show the compatibility between two molecules by visualizing the distance information between them.

본 논문에서는 두 개의 단백질 분자가 결합하여 복합체를 구성할 때, 두 분자 간의 접촉 영역을 발견하여 3차원 공간에서 가시화하는 방법을 제시한다. 두 분자 간의 접촉 영역은 기하학적인 측면에서 서로 상보성을 보이며, 상보적인 결합의 크기를 나타내기 위한 방법으로 접촉 영역의 면적을 계산하는 방법이 주로 사용되어 왔다. 접촉 영역의 면적을 수치화한 결과와 접촉 영역의 단순 표시는 서로 다른 접촉 영역에 대해 상대적인 결합 강도를 비교하기에는 적합하지만, 접촉 영역이 가진 기하학적인 특성을 분석하기에는 부적합하다. 본 논문에서는 접촉 영역에서 상보성을 표시하기 위해 상대 분자와의 거리 정보를 가시화하는 방법을 제시한다.

Keywords

References

  1. D. Levine, M. Facello, P. Hallstrom, G. Reeder, B. Walenz, F. Stevens, "Stalk: an Interactive System for Virtual Molecular Docking," IEEE Computational Science and Engineering, Vol.4, No.2,pp. 55-65, 1997.
  2. T. J. A. Ewing, S. Makino, A. G. Skillman, I. D. Kuntz, "DOCK4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Databases," Journal of Computer-Aided Molecular Design, Vol.15, No.5, pp.411-428, 2001. https://doi.org/10.1023/A:1011115820450
  3. H. Nagata, H. Mizushima, H. Tanaka, "Concept and Prototype of Protein-Ligand Docking Simulator with Force Feedback Technology," Bioinformatics, Vol.18, No.1, pp.140-146, 2002. https://doi.org/10.1093/bioinformatics/18.1.140
  4. R. D. Taylor, P. J. Jewsbury, J. W. Essex, "A Review of Protein-Small Molecule Docking Methods," Journal of Computer-Aided Molecular Design, Vol.16, No.3, pp.151-166, 2002. https://doi.org/10.1023/A:1020155510718
  5. C. M. Venkatachalam, X. Jiang, T. Oldfield, M. Waldman, "LigandFit: a Novel Method for the Shape-Directed Rapid Docking of Ligands to Protein Active Sites," Journal of Molecular Graphics and Modelling, Vol.21, No.4, pp.289-307, 2003. https://doi.org/10.1016/S1093-3263(02)00164-X
  6. S. K. Lai-Yuen, Y.-S. Lee, "Interactive Computer-Aided Design for Molecular Docking and Assembly," Computer-Aided Design and Applications, Vol.3, No.6, pp.701-709, 2006. https://doi.org/10.1080/16864360.2006.10738423
  7. Y. Zhao, M. F. Sanner, "Protein-Ligand Docking with Multiple Flexible Side Chains," Journal of Computer Aided Molecular Design, Vol.22, No.9, pp.673-679, 2008. https://doi.org/10.1007/s10822-007-9148-5
  8. O. Trott, A. J. Olson, "AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading," Journal of Computational Chemistry, Vol.31, No.2, pp.455-461, 2010.
  9. S. Gong, G. Yoon, I. Jang, D. Bolser, P. Dafas, M. Schroeder, H. Choi, Y. Cho, K. Han, S. Lee, "PSIbase: a database of protein structural interactome map (PSIMAP)," Bioinformatics, Vol.21, No.10, pp.2541-2543, 2005. https://doi.org/10.1093/bioinformatics/bti366
  10. J. Park, M. Lappe, S. Teichmann, "Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast," J. Mol. Biol., Vol.307, pp.929-938, 2001. https://doi.org/10.1006/jmbi.2001.4526
  11. M. Lappe, J. Park, O. Niggemann, L. Holm, "Generating protein interaction maps from incomplete data: application to Fold assignment," Bioinformatics, pp.149-156, 2001.
  12. K. S. Han, B. K. Park, H. G. Kim, J. S. Hong, J. Park, "HPID: The Human Protein Interaction Database," Bioinformatics, Vol.20, pp.2466-2470, 2004. https://doi.org/10.1093/bioinformatics/bth253
  13. T. M. W. Nye, C. Berzuini, W. R. Gilks, M. M. Babu, S. Teichmann, "Predicting the strongest domain-domain contact in interacting protein pairs," Statistical Applications in Genetics and Molecular Biology, Vol.5, No.1, 2006.
  14. G. Steinkellner, R. Rader, G. G. Thallinger, C. Kratky, K. Gruber, "VASCo: computation and visualization of annotated protein surface contacts," BMC Bioinformatics, Vol.10, No.32, 2009.
  15. S. Arab, M. Sadeghi, C. Eslahchi, H. Pezeshk, A. Sheari, "A pairwise residue contact area-based mean force potential for discrimination of native protein structure," BMC Bioinformatics, Vol.11, No.16, 2010.