Molecular Level Data Interpretation and Interaction Pathway Modeling Using 3-D Visualization
Jin-Young Hong (1), Alfred H. Merrill, Jr. (2), May D. Wang(1)
(1) Wallace H. Coulter Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory Univ.; (2)School of Biology, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, GA 30332

We have developed an advanced 3-D interactive visualization system to assist the molecular and cell experimental biologist to interpret the experimental data in an intuitive, visible, and real-time manner. The data are acquired by advanced biotechnologies such as DNA microarray, metabolomic mass spectrometor, confocal imaging, and nanoimaging quantum dot (QD) imaging data. The molecular interaction requires (1) representing known pathways based on existing experimental data; (2) predicting of interesting new pathways to the experimental biologists for wet-lab validation; and (3) ultimately assisting novel pathway discovery and annotation to database. The system is designed with the ideas of creating a human-knowledge-based intelligent computation framework, and it is intended to serve the experimental scientist in the discovery process. The system is also designed to be user-friendly, robust, dynamics, and effectives in modeling molecular interaction such as pathway model. Some example features are (1) linking the dynamic modeling module with the visualization module, and using animation to illustrate the state transition; (2) highlighting relevant feedforward or feedback paths according to the experimental design focus; (3) designing a dynamic visualization drawing algorithm that can automatically inference new pathway for experimental validation, and upon verification, will be annotated to store in pathway databases; and (4) enabling to analyze multiple pathways and display for comparative analysis. The visualization requires high resolution, and real-time performance. Our lab has a 3-D immersive visualization setup that is connected to a high-power HP computing cluster to fulfill the goal. The system is currently undergoing in-house user feedback.

LigPro: Rapid Inspection of Protein-Ligand Interactions
Qing Zhang, John L. Moreland, Apostol Gramada, John Beaver, and Philip E. Bourne
San Diego Supercomputer Center

We present LigPro, an easy to use 3D software tool designed for examining protein-ligand interactions, such as H-bond interactions, hydrophobic interactions and ligand-protein interactions bridged by ordered H2O. LigPro was built in Java and uses the molecular biology tool kit (mbt). It takes a standard Protein Data Bank file or a mmCIF structure file as input, dynamically generates the ligand list associated with the structure, automatically centers the view at the user-selected ligand and provides one-click inspections of different types of interactions. LigPro provides two-way communication between its sequence and structure viewers, i.e. click on any residue in the sequence viewer, the residue will be drawn or highlighted in the structure viewer; click on any fragment/residue in the structure viewer, the corresponding sequence will be highlighted in the sequence viewer. LigPro has been integrated into the RCSB PDB site, where it runs as a java applet. It can also be run as a standalone application on desktop to access local structure files and files on PDBs servers; we implemented Java Web Start to provide a one-click download and automatic updates of this application on the client side. Besides rapid inspection of protein-ligand interactions, LigPro can also be used to produce high quality images for publications.

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