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Molecular Docking with a View: The Integration of a Monte Carlo Docking Program into a Virtual Reality Environment | Springer Nature Link

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Trevor N. Hart, Richard E. Gillilan, Ryan Lilien, Steven R. Ness & Randy J. Read

Part of the book series: The Springer International Series in Engineering and Computer Science ((SECS,volume 478))

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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.

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Author information Author notes

Ryan Lilien

Present address: Department of Computer Science, Dartmouth College, USA

Steven R. Ness

Present address: Department of Biochemistry, University of British Columbia, Canada

Authors and Affiliations

Department of Medical Microbiology and Immunology, University of Alberta, Canada

Trevor N. Hart, Steven R. Ness & Randy J. Read

Cornell Theory Center, Cornell University, USA

Richard E. Gillilan & Ryan Lilien

Editor information Editors and Affiliations

University of Alberta, Canada

Jonathan Schaeffer

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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

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