Abstract
During docking, protein molecules and other small molecules interact together to form transient macromolecular complexes. Docking is an integral part of structure-based drug design and various docking programs are used for in-silico docking. Although these programs have powerful docking algorithms, they have limitations in the three-dimensional visualization of molecules. An immersive environment would bring additional advantages in understanding the molecules being docked. It would enable scientists to fully visualize molecules to be docked, manipulate their structures and manually dock them before sending to new conformations to a docking algorithm. This could greatly reduce docking time and resource consumption. Being an exhaustive process, parallelization of docking is of utmost importance for faster processing. This paper proposes the use of a collaborative and immersive environment for initially hand docking molecules and which then uses powerful algorithms in existing parallelized docking programs to decrease computational docking time and resources.
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Cruz-Neira, C., Sandin, D.J., Defanti, T.A., Kenyon, R.V., Hart, J.C.: The CAVE: Audio visual experience automatic virtual environment Subsequences. Communications of ACM 35, 64–72 (1992)
Cruz-Neira, C., Langley, R., Bash, P.A.: VIBE: a virtual biomolecular environment for interactive molecular modeling Subsequences. Computers and Chemistry 20, 469–477 (1996)
Levine, D., Facello, M., Hallstrom, P., Reeder, G., Walenz, B., Stevens, F.: Stalk: An interactive system for virtual molecular docking Subsequences. IEEE Computations Science and Engineering, 55–56 (1997)
Tolmie, D., Renwick, J.: HIPPI: simplicity yields success, Subsequences. Network IEEE 7, 28–32 (1993)
Chastin, J., Zhu, Y., Brooks, J., Owen, S., Harrison, R.: A collaborative multi-view virtual environment for molecular visualization and modeling. In: 3rd International Conference on Coordinated and Multiple Views in Exploratory Visualization (CVM), pp. 77–84. IEEE, London (2005)
Chastin, J., Zhu, Y., Brooks, J., Owen, S., Harrison, R.: AMMP-Vis: A collaborative virtual environment for molecular modeling. In: ACM Symposium on Virtual Reality Software and Technology, Monterey, pp. 8–15 (2005)
Ma, W., Zhu, Y., Harrison, R., Owen, G.S.: AMMP-EXTN: Managing user privacy and cooperation demand in a collaborative molecule modeling virtual system. In: Virtual Reality Conference VR 2007, pp. 301–302. IEEE, Los Alamitos (2007)
Ma, W.: AMMP-EXTN: a user privacy and collaboration control framework for a multi-user collaboratory virtual reality system. Masters Thesis, Georgia State University (December 2007)
Abagyan, R.A., Totrov, M.M.: Biased probability Monte Carlo conformation searches and electrostatic calculations and peptides and proteins Subsequences. J. Mol. Biol. 235, 983–1002 (1994)
Holland, J.: Adaptation in Natural and Artificial Systems Infrastructure. University of Michigan Press, Ann Arbor (1975)
Bland, J.A., Dawson, G.P.: Tabu search and design optimization Subsequences. Computer Aided Design 23, 195–201 (1991)
Goodsell, D.S., Olson, A.J.: Automated docking of substrates to proteins by simulated annealing Subsequences. Proteins: Structure, Function and Genetics 8, 195–202 (1990)
Sousa, S.F., Fernandes, P.A., Ramas, M.J.: Protein-ligand docking: current status and future challenges Subsequences. Proteins: Structure, Function and Bioinformation 65, 15–26 (2006)
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer Jr, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M.: Protein Data Bank: A computer-based archival file for macromolecular structures Subsequences. J. Mol. Biol. 112, 534–542 (1997)
Berman, H.M., Westbrook, J., Feng, Z., Gillilands, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank Subsequences. Nucleic Acids Research 28, 235–242 (2000)
Khodade, P., Prabhu, R., Chandra, N., Raha, S., Govindarajan, R.: Parallel Implementation of Autodock Subsequences. J. Appl. Cryst. 40, 598–599 (2007)
Zhang, S., Kumar, K., Jiang, X., Wallqvist, A., Reifman, J.: DOVIS: an implementation for high-throughput virtual screening using AutoDock Subsequences. BMC Bioinformatics 9, 126 (2008)
Haffegee, A.: VieGen: an accessible toolset for the configuration and control of virtual environments Ph.D Thesis, University of Reading (2008)
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Nadan, T., Haffegee, A., Watson, K. (2009). Collaborative and Parallelized Immersive Molecular Docking. In: Allen, G., Nabrzyski, J., Seidel, E., van Albada, G.D., Dongarra, J., Sloot, P.M.A. (eds) Computational Science – ICCS 2009. ICCS 2009. Lecture Notes in Computer Science, vol 5545. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-01973-9_82
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DOI: https://doi.org/10.1007/978-3-642-01973-9_82
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