Paper Citing NAMD - Abstract
Wang, Li; Wan, Huagen; Peng, Qunsheng; Chen, Xin; Wu, Tao; Wang, Junhui
Volumetric Visualization and Analysis of Molecular Interaction Field
2009 3RD INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1-11, 852-855, 2009
Electrostatic and van der Waals interactions are of central importance for many biological processes. Yet it is difficult to visualize and analyze the two interactions with existing graphical representations of proteins such as wireframe, VDW, and molecular surface due to the three-dimensional nature of protein interaction distribution. The molecular interaction field (MIF) is defined as a three-dimensional uniform grid surrounding a protein of known structure with its every grid point storing the interaction of a probe with the protein. It would be more straightforward to volumetrically visualize and analyze the MIF for understanding of protein structure and function than existing graphical representations of proteins. A novel method for volumetrically visualizing and analyzing the MIF of a protein is proposed. The ray-casting algorithm is used to visualize the MIF to achieve convincing rendering effect and produce informative images that reveal the M IF volume features. The volume rendering results are used to analyze two example proteins, i.e., the HIV-1 protease (pdb id: 1a30) and the Dps protein (pdb id: 1dps), with biologically meaningful results being derived.
