title: A collaborative visual analytics suite for protein folding research.
abstract: Molecular dynamics (MD) simulation is a crucial tool for understanding principles behind important biochemical processes such as protein folding and molecular interaction. With the rapidly increasing power of modern computers, large-scale MD simulation experiments can be performed regularly, generating huge amounts of MD data. An important question is how to analyze and interpret such massive and complex data. One of the (many) challenges involved in analyzing MD simulation data computationally is the high-dimensionality of such data. Given a massive collection of molecular conformations, researchers typically need to rely on their expertise and prior domain knowledge in order to retrieve certain conformations of interest. It is not easy to make and test hypotheses as the data set as a whole is somewhat "invisible" due to its high dimensionality. In other words, it is hard to directly access and examine individual conformations from a sea of molecular structures, and to further explore the entire data set. There is also no easy and convenient way to obtain a global view of the data or its various modalities of biochemical information. To this end, we present an interactive, collaborative visual analytics tool for exploring massive, high-dimensional molecular dynamics simulation data sets. The most important utility of our tool is to provide a platform where researchers can easily and effectively navigate through the otherwise "invisible" simulation data sets, exploring and examining molecular conformations both as a whole and at individual levels. The visualization is based on the concept of a topological landscape, which is a 2D terrain metaphor preserving certain topological and geometric properties of the high dimensional protein energy landscape. In addition to facilitating easy exploration of conformations, this 2D terrain metaphor also provides a platform where researchers can visualize and analyze various properties (such as contact density) overlayed on the top of the 2D terrain. Finally, the software provides a collaborative environment where multiple researchers can assemble observations and biochemical events into storyboards and share them in real time over the Internet via a client-server architecture. The software is written in Scala and runs on the cross-platform Java Virtual Machine. Binaries and source code are available at http://www.aylasoftware.org and have been released under the GNU General Public License.
authors: Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, United States. Electronic address: harveywi@cse.ohio-state.edu.
authors: William
authors: W
authors: Harvey
authors: Chemical Physics Program, The Ohio State University, Columbus, OH, United States.
authors: In-Hee
authors: IH
authors: Park
authors: Visualization Group, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
authors: Oliver
authors: O
authors: Rübel
authors: Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States.
authors: Valerio
authors: V
authors: Pascucci
authors: Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA, United States.
authors: Peer-Timo
authors: PT
authors: Bremer
authors: Chemical Physics Program and College of Pharmacy, The Ohio State University, Columbus, OH, United States.
authors: Chenglong
authors: C
authors: Li
authors: Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, United States. Electronic address: yusu@cse.ohio-state.edu.
authors: Yusu
authors: Y
authors: Wang
mesh_terms: D003196:Computer Graphics; D056004:Molecular Dynamics Simulation; D058977:Molecular Sequence Annotation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins
keywords: Molecular simulation data; Visualization tool