Abstract
Molecular docking has become a fundamental tool in both the process of drug discovery and the understanding of protein structure and function. While much effort has gone into faster and more effective automated docking algorithms, the visualization of molecular structures remains an important tool for the correct interpretation of structural predictions. The integration of the Research docking algorithm into the Virtual Reality facility at the Cornell Theory Center offers a unique tool for understanding of protein-ligand interactions. The docking program Research is a fast Monte Carlo docking method employing a full force-field interaction model to represent molecular interactions. The program is integrated as a function call within the VR/3D workspace environment and connected with a sophisticated molecular viewer that displays docking results in real time. The workspace viewer allows the user to change perspective, style of molecular display, and parameters of the Research algorithm during the docking procedure. Multiple docking processes can be run simultaneously and interactively attached or detached from the viewing workspace. The integrated docking/viewing environment is not only a practical tool for drug discovery and design, but also offers an inside look at the molecular docking process.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Bergman, L., Richardson, J., and Brooks, F. (1993). VIEW: An exploratory molecular visualization system with user-definable interaction sequences. In SIGGRAPH’93, pages 117–126.
Blaney, J. and Dixon, J. (1993). A good ligand is hard to find: Automated docking methods. Persp. Drug Dis. Des., 1:301–319.
Brooks, C., Karplus, M., and Pettitt, B. (1988). Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. Advances in Chemical Physics, Vol 71. Wiley & Sons, NY.
Brooks, F., Ouh-Young, M., NJ, J., and Kilpatrick, P. (1990). Project grope: Haptic displays for scientific visualization. In SIGGRAPH’90, pages 177–185.
Cantor, C. and Schimmel, P. (1980). Biophysical Chemistry, Part 1: The Conformation of Biological Macromolecules. W.H. Freeman and Company, New York.
Cruz-Neira, C. (1995). Virtual reality based on multiple projection screens: the CAVE and its applications to computational science and engineering. PhD thesis, University of Illinois at Chicago. University Microfilms International #9532383.
Cruz-Neira, C., Langley, R., and Bash, P. (1996). VIBE: A virtual biomolecular environment for interactive molecular modeling. Computers and Chemistry, 20:469. http://www.cs.uiowa.educremer/sive95/.sive-sessions.html .
Cruz-Neira, C., Sandin, D., and DeFanti, T. (1993). Surround-screen projection-basedvirtual reality: The design and implementation of the CAVE. In SIGGRAPH’93.
Dixon, J. (1997). Evaluation of the CASP2 docking section. Proteins, Suppl., 1:198–204.
Gillilan, R. and Ripoll, D. (1995). Vizualizing enzyme electrostatics with IBM visualization data explorer. In Bowie, J. E., editor, Data Visualization in Molecular Science. Addison-Wesley, New York.
Hart, T., Ness, S., and Read, R. (1997). Critical evaluation of the Research docking program for the CASP2 challenge. Proteins, Suppl., 1:205–209.
Hart, T., Ness, S., and Read, R. (1998). Monte Carlo docking of flexible ligands using multiple conformations. Manuscript in preparation.
Hart, T. and Read, R. (1992). A multiple-start Monte Carlo docking method. Proteins, 13:206–222.
Hart, T. and Read, R. (1994). Multiple-start Monte Carlo docking of flexible ligands. In Merz, K. and LeGrand, S., editors, The Protein Folding Problem and Tertiary Structure Prediction, pages 71–108. Birkhäuser, Boston.
Hunter, W., Bailey, S., Habash, J., Harrop, S., Helliwell, J., Abogye-Kwarteng, T., Smith, K., and Fairlamb, A. (1992). Active site of trypanothione reductase: a target for rational drug design. J. Mol. Biol., 227:322–333.
Ihlenfeldt, W. (1997). Virtual reality in chemistry. J. Mol. Model., 3:386–402.
Jacoby, E., Schlichting, I., Lantwin, C., Kabsch, W., and Krauth-Siegel, R. (1996).Crystal structure of the Trypanosoma cruzi trypanothione reductase-mepacrine complex. Proteins, 24:73–80.
Kersten, S., Reczek, P., and Noy, N. (1997). The tetramerization region of the retinoid X receptor is important for transcriptional activation by the receptor. J. Biol. Chem., 272:29759–29768.
Kirkpatrick, S., Gelatt, C., and Vecchi, M. (1983). Optimization by simulated annealing. Science, 220:671–680.
Leech, J., Prins, J., and Hermans, J. (1996). SMD: Visual steering of molecular dynamics for protein design. IEEE Computational Science and Engineering, pages 38–45.
Ponasik, J., Strickland, C., Faerman, C., Savvides, S., Karplus, P., and Ganem, B. (1995). Selective inhibitors of crithidia-faciculata trypanothione reductase. Biochemical Journal Part 2, 311:371–375.
Priestle, J., Fassler, A., Rosel, J., Tintelnot-Blomley, M., Strop, P., and Grutter, M. (1995). Comparative analysis of the x-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 53820, a novel pseudosymmetric inhibitor. Structure, 3:381–389.
Schirmer, R., Muller, J., and Krauth-Siegel, R. (1995). Disulfide-reductase inhibitors as chemotherapeutic agents: The design of drugs for trypanosomiasis and malaria. Angew. Chem. Int. Ed. Engl., 34:141–154.
Stryer, L. (1981). Biochemistry. W.H. Freeman, San Francisco.
Subbiah, S. and Harrison, S. (1989). A simulated annealing approach to the search problem of protein crystallography. Acta Cryst., A45:337–342.
Suries, M., Richardson, J., Richardson, D., and Brooks, F. (1994). Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling system. Protein Science, 3:198–210.
Varshney, A., Brooks, F., and Wright, W. (1994). Linearly scalable computation of smooth molecular surfaces. IEEE Computer Graphics Applications, 14:19–25.
Wilson, S. and Cui, W. (1990). Applications of simulated annealing to peptides. Biopolymers, 29:225–235.
Wood, F., Brown, D., Amidon, R., Alferness, J., Joseph, B., Gillilan, R., and Faerman, C. (1996). Workspace and the study of Chagas’ disease. IEEE Computer Graphics and Applications, 16:72–78.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1998 Springer Science+Business Media New York
About this chapter
Cite this chapter
Hart, T.N., Gillilan, R.E., Lilien, R., Ness, S.R., Read, R.J. (1998). Molecular Docking with a View: The Integration of a Monte Carlo Docking Program into a Virtual Reality Environment. In: Schaeffer, J. (eds) High Performance Computing Systems and Applications. The Springer International Series in Engineering and Computer Science, vol 478. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-5611-4_30
Download citation
DOI: https://doi.org/10.1007/978-1-4615-5611-4_30
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-7567-8
Online ISBN: 978-1-4615-5611-4
eBook Packages: Springer Book Archive