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A system for data-driven layout and exploration of molecular dynamics simulations

Robert Patro
Cheuk Yiu Ip
Sujal Bista
Samuel S. Cho
D. Thirumalai
Amitabh Varshney

MDMap is a system designed to summarize long-running molecular dynamics (MD) simulations. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. 

Release Date:
Data type:
2D, 3D, Network / hierarchy graph

Project development

Institution: University of Maryland, College Park, Wake Forest University

This work has been supported in part by the NSF grants: CNS 04–03313, CCF 05–41120, CMMI 08–35572, NSF 09–59979, NSF 09–14033, NIH grant GM 076688–08 and the NVIDIA CUDA Center of Excellence. Samuel S. Cho is supported by the Wake Forest University Science Research Fund. Any opinions, findings, conclusions, or recommendations expressed in this article are those of the authors and do not necessarily reflect the views of the research sponsors.