poster

A playful tool for predicting protein-protein docking

Authors:

Tatsuo Nakajima,

Yutaka AkiyamaAuthors Info & Claims

MUM '19: Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia

Article No.: 40, Pages 1 - 5

https://doi.org/10.1145/3365610.3368409

Published: 26 November 2019 Publication History

Abstract

In this paper, we propose a playful tool to predict protein-protein docking. The tool uses human bodies to explore better protein-protein docking, where it offers natural interactions to dock protein molecules in a flexible way and playful interactions through two users' cooperative body movements. We present the design and implementation of the proposed tool and show potential opportunities and pitfalls of the current tool.

References

[1]

Florian Alt, Sabrina Geiger, and Wolfgang Höhl. 2018. ShapelineGuide: Teaching Mid-Air Gestures for Large Interactive Displays. In Proceedings of the 7th ACM International Symposium on Pervasive Displays (PerDis '18), Albrecht Schmidt, Julie R. Williamson, Ivan Elhart, Matthias Baldauf, Mateusz Mikusz, Salvatore Sorce, Katja Kurdyukova, Passant El.Agroudy, and Vito Gentile (Eds.). ACM, New York, NY, USA, Article 3, 8 pages.

Digital Library

[2]

Patrick Bader, Alexandra Voit, Huy Viet Le, Paweł W. Woźniak, Niels Henze, and Albrecht Schmidt. 2019. WindowWall: Towards Adaptive Buildings with Interactive Windows as Ubiquitous Displays. ACM Trans. Comput.-Hum. Interact. 26, 2, Article 11 (March 2019), 42 pages.

Digital Library

[3]

Helen M. Berman, The Protein Data Bank: a historical perspective. Acta Crystallographica Section A. A64 (1): 88--95.

[4]

Anne Bowser, Derek Hansen, Yurong He, Carol Boston, Matthew Reid, Logan Gunnell, and Jennifer Preece. 2013. Using gamification to inspire new citizen science volunteers. In Proceedings of the First International Conference on Gameful Design, Research, and Applications (Gamification '13). ACM, New York, NY, USA, 18--25. http://doi.acm.org/10.1145/2583008.2583011

Digital Library

[5]

Li-Chieh Chen, Yun-Maw Cheng, Po-Ying Chu, and Frode Eika Sandnes. 2017. Identifying the Usability Factors of Mid-Air Hand Gestures for 3D Virtual Model Manipulation. In Universal Access in Human-Computer Interaction. Designing Novel Interactions, Margherita Antona and Constantine Stephanidis (Eds.). Springer International Publishing, Cham, 393--402.

[6]

Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popovic, and Foldit players. 2010. Predicting protein structures with a multiplayer online game. Nature, Vol. 466, No. 7307, pp. 756--760.

[7]

Haiyou Deng, Ya Jia, and Yang Zhang. 2018. Protein structure prediction. International Journal of Modern Physics B, Vol.32, No.18.

[8]

Sebastian Deterding, Dan Dixon, Rilla Khaled, and Lennart Nacke. 2011. From game design elements to gamefulness: defining "gamification". In Proceedings of the 15th International Academic MindTrek Conference: Envisioning Future Media Environments (MindTrek '11). ACM, New York, NY, USA, 9--15.

Digital Library

[9]

Thomas D. Goddard, Alan A. Brilliant, Thomas L. Skillman, Steven Vergenz, James Tyrwhitt-Drake, Elaine C. Meng, Thomas E. Ferrin. 2018. Molecular Visualization on the Holodeck, Journal of Molecular Biology, Volume 430, Issue 21, pp.3982--3996

[10]

Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. 2018. MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. BMC Bioinformatics. Vol.19(Suppl 4), No.62

[11]

Susanne Hecker, Muki Haklan, Anne Bowser, Zen Makuch, Johannes Vogel, Aletta Bonn. 2018. Citizen Science: Innovation in Open Science, Society and Policy. UCLPRESS

[12]

Jesper Juul. 2012. A Casual Revolution: Reinventing Video Games and Their Players. MIT Press.

[13]

Julia Kelemen-Finan, Martin Scheuch & Silvia Winter. 2018. Contributions from citizen science to science education: an examination of a biodiversity citizen science project with schools in Central Europe, International Journal of Science Education, Vol. 40, No.17, pp.2078--2098

[14]

Risa Kimura and Tatsuo Nakajima. 2018. Sharing Collective Human's Eye Views for Stimulating Reflective Thinking. In Proceedings of the 17th International Conference on Mobile and Ubiquitous Multimedia (MUM 2018), Slim Abdennadher and Florian Alt (Eds.). ACM, New York, NY, USA, 341--349.

Digital Library

[15]

Risa Kimura, Tatsuo Nakajima. 2020. A Case Study of Virtualizing the Real World: Virtualizing Collective Human's Eyesight Capabilities. In Proceedings of the 8th International Conference on Distributed, Ambient and Pervasive Interactions.

[16]

Brian Koepnick, Jeff Flatten, Tamir Husain, AlexFord, Daniel-Adriano Silva, Matthew J. Bick, Aaron Bauer, Gaohua Liu, Yojiro Ishida, Alexander Boykov, Roger D. Estep, Susan Kleinfelter, Toke Nørgård-Solano, Linda Wei, Foldit Players, Gaetano T. Montelione, Frank DiMaio, Zoran Popović, Firas Khatib, Seth Cooper, David Baker. 2019. De novo protein design by citizen scientists, Nature, 570, 7761, pp.390--394.

[17]

Guillaume Levieux, Guillaume Tiger, Stephanie Mader, Jean-Fraņcois Zagury, Stephane Natkin, and Matthieu Montes. 2014. Udock, the interactive docking entertainment system. Faraday discussions, Vol. 169, pp. 425--441.

[18]

Tom Lunt and John Curran. 2010. 'Are you listening please?' The advantages of electronic audio feedback compared to written feedback. Assessment & Evaluation in Higher Education, Vol.35, No.7. pp.759--769.

[19]

Yuki Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Yatake Akiyama. 2016. Advances in Biochemical Engineering/Biotechnology, In: Nookaew I. (eds) Network Biology. Advances in Biochemical Engineering/Biotechnology, Vol. 160. Springer.

[20]

Tatsuo Nakajima and Vili Lehdonvirta. 2013. Designing motivation using persuasive ambient mirrors. Personal Ubiquitous Comput. Vol.17, No.1 (January 2013), 107--126.

Digital Library

[21]

Scott Nicholson. 2012. A User-Centered Theoretical Framework for Meaningful Gamification, In Proceedings of Game+Leaning+Socoety 8.0.

[22]

Fatemeh Noroozi, Ciprian Adrian Corneanu, Dorota Kamińska, Tomasz Sapiński, Sergio Escalera, Gholamreza Anbarjafari. 2018. Survey on Emotional Body Gesture Recognition, arXiv:1801.07481.

[23]

Magnus S Norrby, Christoph Grebner, Joakim Eriksson, Jonas Boström. 2015. Molecular Rif: Virtual Reality for Drug Designers. Journal of Chemical Information and Modeling, Journal of Chemical Information and Modeling, Vol.55, No.11.

[24]

Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, and Yutaka Akiyama. 2014. MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data. Protein and Peptide Letters, Vol.21, No.8, pp.766--778.

[25]

Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. 2014. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. Bioinformatics. Vol.30, No.22. pp.3281--3283.

[26]

Maaret Posti, Leena Ventä-Olkkonen, Ashley Colley, Olli Koskenranta, and Jonna Häkkilä. 2014. Exploring Gesture Based Interaction with a Layered Stereoscopic 3D Interface. In Proceedings of The International Symposium on Pervasive Displays (PerDis '14), Sven Gehring (Ed.). ACM, New York, NY, USA, Pages 200, 2 pages.

Digital Library

[27]

Mizuki, Sakamoto, Tatsuo Nakajima and Sayaka Akioka. 2017. Gamifying collective human behavior with gameful digital rhetoric. Multimedia Tools and Applications, Vol. 76, No.10 (May 2017), pp.12539--12581.

Digital Library

[28]

Stefan Schneegass and Alexandra Voit. 2016. GestureSleeve: using touch sensitive fabrics for gestural input on the forearm for controlling smartwatches. In Proceedings of the 2016 ACM International Symposium on Wearable Computers (ISWC '16). ACM, New York, NY, USA, pp.108--115.

Digital Library

[29]

Stuart T. Smith, Catherine Sherrington, Stuart Studenski, Daniel Schoene, Stephen R Lord. 2009. A novel Dance Dance Revolution (DDR) system for in-home training of stepping ability: Basic parameters of system use by older adults. British Journal of Sports Medicine. Vol.45, No.5. pp.441--445.

[30]

Rejane Spitz, Clorisval Pereira Jr., Francisco Queiroz, Leonardo C. Leite, Peter Dam, Marcelo P. Ferranti, Renan Kogut, Wesley Oliveira. 2017. Gamification, citizen science and civic engagement: in search of the common good. In Proceedings of the 6th BALANCE-UNBALANCE 2017 [Arts + Sciences x Technology = Environment / Responsibility] A Sense of Place.

[31]

Andy Thomason, Ioannis Filippis, Pedro Quijada Leyton, Michael Sternberg, William Latham, and Frederic Fol Leymarie. Bioblox: Protein docking game. Heidelberg, Germany. Available: http://bioblox.org/ (Accessed June 29, 2019)

[32]

Adrien Treuille, Rhiju Das. 2014. Scientific rigor through videogames. Trends in Biochemical Sciences, Vol. 39, No. 11, pp.507--509.

[33]

Luis von Ahn and Laura Dabbish. 2008. Designing games with a purpose. Commun. ACM 51, 8 (August 2008), pp.58--67.

Digital Library

[34]

Andrew M. Wollacott, Kenneth M. Merz Jr. 2007. Haptic applications for molecular structure manipulation. Journal of Molecular Graphics and Modelling. Vol.25, No.6. pp.801--805.

[35]

Unity: the Game Development Platform, Available: https://unity.com/ (Accessed October 1)

Cited By

Kimura RJiang KZhang DNakajima T(2021)Society of “Citizen Science through Dancing”Ambient Intelligence – Software and Applications10.1007/978-3-030-58356-9_2(13-23)Online publication date: 2021
https://doi.org/10.1007/978-3-030-58356-9_2
Kimura RJiang KZhang DNakajima T(2020)A Playful Citizen Science Tool for Casual UsersProceedings of the 2020 International Conference on Advanced Visual Interfaces10.1145/3399715.3399937(1-3)Online publication date: 28-Sep-2020
https://dl.acm.org/doi/10.1145/3399715.3399937

Index Terms

A playful tool for predicting protein-protein docking
1. Human-centered computing
  1. Human computer interaction (HCI)

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Information & Contributors

Information

Published In

cover image ACM Other conferences

MUM '19: Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia

November 2019

462 pages

ISBN:9781450376242

DOI:10.1145/3365610

General Chair:
Fabio Paternò
CNR-ISTI, Italy
,
Program Chairs:
Giulio Jacucci
University of Helsinki, Finland
,
Michael Rohs
University of Hannover, Germany
,
Carmen Santoro
CNR-ISTI, Italy

Copyright © 2019 Owner/Author.

Permission to make digital or hard copies of part or all 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 third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 26 November 2019

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MUM 2019

MUM 2019: 18th International Conference on Mobile and Ubiquitous Multimedia

November 26 - 29, 2019

Pisa, Italy

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Cited By

Kimura RJiang KZhang DNakajima T(2021)Society of “Citizen Science through Dancing”Ambient Intelligence – Software and Applications10.1007/978-3-030-58356-9_2(13-23)Online publication date: 2021
https://doi.org/10.1007/978-3-030-58356-9_2
Kimura RJiang KZhang DNakajima T(2020)A Playful Citizen Science Tool for Casual UsersProceedings of the 2020 International Conference on Advanced Visual Interfaces10.1145/3399715.3399937(1-3)Online publication date: 28-Sep-2020
https://dl.acm.org/doi/10.1145/3399715.3399937

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