HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data
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Abstract
Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.
Keywords
Data sharing Data publishing Data streaming Graphical processing unit Webgl Web application Interactive structure Interactive dynamicsNotes
Acknowledgements
The authors want to acknowledge all the persons involved in the review process. Their comments have helped to greatly improve this report and the functionality of the tool.
Funding
This work has been supported by the Consejo Nacional de Ciencia y Tecnología México (Grant Number 132376 to M.C.-T.).
References
- 1.Perilla JR, Goh BC, Cassidy CK, Liu B, Bernardi RC, Rudack T, Yu H, Wu Z, Schulten K (2015) Curr Opin Struct Biol 31:64–74CrossRefPubMedPubMedCentralGoogle Scholar
- 2.Venable RM, Brown FL, Pastor RW (2015) Chem Phys Lipids 192:60–74CrossRefPubMedPubMedCentralGoogle Scholar
- 3.Wang X, Wang Y, Zheng L, Chen J (2014) Curr Med Chem 21:1968–1975CrossRefPubMedPubMedCentralGoogle Scholar
- 4.Zhao H, Caflisch A (2015) Eur J Med Chem 91:4–14CrossRefPubMedPubMedCentralGoogle Scholar
- 5.Aci-Sèche S, Ziada S, Braka A, Arora R, Bonnet P (2016) Future Med Chem 8:545–566CrossRefPubMedPubMedCentralGoogle Scholar
- 6.Bernardi RC, Melo MC, Schulten K (1850) Biochim Biophys Acta 2015:872–877Google Scholar
- 7.Weng J, Wang W (2014) Adv Exp Med Biol 805:305–329CrossRefPubMedPubMedCentralGoogle Scholar
- 8.Kalyaanamoorthy S, Chen YP (2014) Prog Biophys Mol Biol 114:123–136CrossRefPubMedPubMedCentralGoogle Scholar
- 9.Vlachakis D, Bencurova E, Papangelopoulos N, Kossida S (2014) Adv Protein Chem Struct Biol 94:269–313CrossRefPubMedPubMedCentralGoogle Scholar
- 10.Abraham MJ, Murtola T, Schulz R, Pall S, Smith JC, Hess B, Lindahl E (2015) SoftwareX 1–2:19–25CrossRefGoogle Scholar
- 11.Brooks BR (2009) J Comput Chem 30:1545–1614CrossRefPubMedPubMedCentralGoogle Scholar
- 12.Salomon-Ferrer R, Case DA, Walker RC (2013) Wiley Interdiscip Rev: Comput Mol Sci 3:198–210Google Scholar
- 13.Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalac L, Schulten K (2005) J Comput Chem 26:1781–1802CrossRefPubMedPubMedCentralGoogle Scholar
- 14.Humphrey W, Dalke A, Schulten K (1996) J Mol Graphics 14:33–38CrossRefGoogle Scholar
- 15.Schrödinger LLC (2015) The PyMOL Molecular Graphics System, Version 2.0. https://pymol.org/
- 16.Smarr LL, Chien AA, DeFanti T, Leigh J, Papadopoulos PM (2003) Commun ACM 46:58–67CrossRefGoogle Scholar
- 17.Vishwanath V, Burns R, Leigh J, Seablom M (2009) Future Gener Comput Syst 25:184–191CrossRefGoogle Scholar
- 18.Renambot L et al (2004) Sage: the scalable adaptive graphics environment. In: Proceedings of WACE. pp 2004–2009Google Scholar
- 19.Yuan S, Chan HS, Hu Z (2017) Trends Biotechnol 35:559–571CrossRefPubMedPubMedCentralGoogle Scholar
- 20.Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL (2013) Isr J Chem 53:207–216CrossRefGoogle Scholar
- 21.Mwalongo F, Krone M, Becher M, Reina G, Ertl T (2016) Graph Models 88:57–65CrossRefGoogle Scholar
- 22.Grottel S, Krone M, Mller C, Reina G, Ertl T (2015) IEEE Trans Visual Comput Graphics 21:201–214CrossRefGoogle Scholar
- 23.Tiemann JKS, Guixa-Gonzalez R, Hildebrand PW, Rose AS, Hildebrand PW (2017) Nat Methods 14:1123–1124CrossRefPubMedPubMedCentralGoogle Scholar
- 24.Rose AS, Hildebrand PW (2015) Nucleic Acids Res 43:W576–W579CrossRefPubMedPubMedCentralGoogle Scholar
- 25.Kovachev D, Yu T, Klamma R (2012) Adaptive computation offloading from mobile devices into the cloud. In: 2012 IEEE 10th International symposium on parallel and distributed processing with applications (ISPA), pp 784–791Google Scholar
- 26.Deng S, Huang L, Taheri J, Zomaya AY (2015) IEEE Trans Parallel Distrib Syst 26:3317–3329CrossRefGoogle Scholar
- 27.Hernandez IMT, Viveros AM, Rubio EH (2013) Analysis for the design of open applications on mobile devices. In: International Conference on Electronics, Communications and Computing (CONIELECOMP) 2013. pp 126–131Google Scholar
- 28.Noda-Garcia L, Camacho-Zarco AR, Medina-Ruiz S, Gaytan P, Carrillo-Tripp M, Fulop V, Barona-Gomez F (2013) Mol Biol Evol 30:2024–34CrossRefPubMedPubMedCentralGoogle Scholar
- 29.Antillon A et al (2016) PLoS ONE 11:e0162171CrossRefPubMedPubMedCentralGoogle Scholar
- 30.Carrillo-Tripp M, Feller SE (2005) Biochemistry 44:10164–10169CrossRefPubMedPubMedCentralGoogle Scholar
- 31.McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang L-P, Lane TJ, Pande VS (2015) Biophys J 109:1528–1532CrossRefPubMedPubMedCentralGoogle Scholar