Browse > Article
http://dx.doi.org/10.3745/KTSDE.2013.2.12.899

Three Dimensional Visualization of Contact Region for a Protein Complex  

Kang, Beom Sik (경북대학교 생명과학부)
Kim, Ku-Jin (경북대학교 컴퓨터학부)
Kim, Yukyeong (경북대학교 대학원 컴퓨터학부)
Publication Information
KIPS Transactions on Software and Data Engineering / v.2, no.12, 2013 , pp. 899-902 More about this Journal
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.
Keywords
Protein Molecule; Protein Complex; Contact Region; Contact Area; Compatibility; Visualization; Depth Buffer;
Citations & Related Records
연도 인용수 순위
  • Reference
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.   DOI   ScienceOn
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.   DOI   ScienceOn
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.   DOI   ScienceOn
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.   DOI   ScienceOn
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.   DOI
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.   DOI   ScienceOn
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.   DOI   ScienceOn
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.   DOI   ScienceOn
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.   DOI   ScienceOn
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.