Cited By
View all- Reinaldo IPulungan NDarmadi H(2021)Prototyping "Color in Life" EduGame for Dichromatic Color Blind AwarenessProcedia Computer Science10.1016/j.procs.2021.01.070179(773-780)Online publication date: 2021
GLUBs: games for learning and understanding biology
Pages 119 - 126
Abstract
This paper introduces GLUBs, which are games based on molecular mechanisms that take place in biological systems. Such games make use of interactive 3D graphics, and allow the player to interact with molecular components using simple 2D mouse gestures. They are similar to puzzle games, since the goal is to discover the correct interactions between molecular components. When the correct interactions are found, the player observes a molecular mechanism taking place. GLUBs thus have the potential to communicate much of the growing structural and biochemical knowledge in a fun and interesting way. In the game presented in this paper, the molecular mechanism involves the assisted folding of a protein by a chaperone.
References
[1]
Branden, C. and Tooze, J. 1999. Introduction to protein structure. Garland.
[2]
DeCarlo, D., Finkelstein, A. et al. 2003. Suggestive contours for conveying shape. ACM Trans. Graph. 22, 3 (2003), 848--855.
[3]
Gottschalk, S., Lin, M. C. et al. 1996. OBBTree: a hierarchical structure for rapid interference detection. Proceedings of the 23rd annual conference on Computer graphics and interactive techniques (1996), 171--180.
[4]
Lorensen, W. E. and Cline, H. E. 1987. Marching cubes: A high resolution 3D surface construction algorithm. SIGGRAPH Comput. Graph. 21, 4 (1987), 163--169.
[5]
Ludtke, S. J., Baldwin, P. R. et al. 1999. EMAN: semiautomated software for high-resolution single-particle reconstructions. Journal of structural biology. 128, 1 (Dec. 1999), 82--97.
[6]
Pettersen, E. F., Goddard, T. D. et al. 2004. UCSF Chimera-a visualization system for exploratory research and analysis. Journal of computational chemistry. 25, 13 (Oct. 2004), 1605--12.
[7]
Pintilie, G., Zhang, J. et al. 2009. Identifying components in 3D density maps of protein nanomachines by multi-scale segmentation. Life Science Systems and Applications Workshop, 2009. LiSSA 2009. IEEE/NIH (2009), 44--47.
[8]
Protein Data Bank. http://www.pdb.org.
[9]
Schlick, T. 2002. Molecular Modeling and Simulation: An Interdisciplinary Guide. Springer-Verlag New York, Inc.
[10]
Shomura, Y., Yoshida, T. et al. 2004. Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms. Journal of molecular biology. 335, 5 (Jan. 2004), 1265--78.
[11]
Strauss, P. S., Issacs, P. et al. 2002. The design and implementation of direct manipulation in 3D. SIGGRAPH 2002 Course Notes. (2002).
[12]
Trabuco, L. G., Villa, E. et al. 2008. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure (London, England: 1993). 16, 5 (May. 2008), 673--683.
[13]
Truskey, G. A., Yuan, F. et al. 2009. Transport phenomena in biological systems. Prentice Hall.
[14]
Woolfson, M. M. 1997. An Introduction to X-ray Crystallography. Cambridge University Press.
[15]
Zhang, J., Baker, M. L. et al. 2010. Mechanism of folding chamber closure in a group II chaperonin. Nature. 463, 7279 (Jan. 2010), 379--383.
Index Terms
- GLUBs: games for learning and understanding biology
Recommendations
Halogen bonding in complexes of proteins and non-natural amino acids
We have analyzed the influence of halogen bonding to the stability of complexes of proteins and non-natural amino acids.We employed conservation pattern, structural motif, secondary structure, and solvent accessibility calculation.The roles of key ...
Research Article: Halogen bonding in complexes of proteins and non-natural amino acids
In this work, we have analyzed the influence of halogen bonding to the stability of 44 complexes of proteins and non-natural amino acids. Fluorine- and chlorine-containing non-natural amino acids are more prevalent in the dataset, and an even larger ...
Research article: Cation-π interactions in high resolution protein-RNA complex crystal structures
In this work, we have analyzed the influence of cation-@p interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. ...
Comments
Information & Contributors
Information
Published In
May 2010
282 pages
Copyright © 2010 ACM.
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]
Sponsors
- Algoma University College
In-Cooperation
Publisher
Association for Computing Machinery
New York, NY, United States
Publication History
Published: 06 May 2010
Check for updates
Author Tags
Qualifiers
- Research-article
Conference
Futureplay '10
Sponsor:
Contributors
Other Metrics
Bibliometrics & Citations
Bibliometrics
Article Metrics
- View Citations1Total Citations
- 91Total Downloads
- Downloads (Last 12 months)2
- Downloads (Last 6 weeks)0
Reflects downloads up to 12 Jan 2025
Other Metrics
Citations
Cited By
View all- Reinaldo IPulungan NDarmadi H(2021)Prototyping "Color in Life" EduGame for Dichromatic Color Blind AwarenessProcedia Computer Science10.1016/j.procs.2021.01.070179(773-780)Online publication date: 2021
View Options
Login options
Check if you have access through your login credentials or your institution to get full access on this article.
Sign in