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. 2012 Dec 26;41(3):1483–1495. doi: 10.1093/nar/gks1302

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© The Author(s) 2012. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.

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Figure 2. — Computational procedure for modeling multiple four-way RNA junction structures. (1) Multiple four-way RNA junction structures are separated into individual RNA junction as input. (2) Each junction is analyzed for 2D helical arrangements based on coaxial stacking and junction family type in conjunction with Junction-Explorer. (3) These topologies are processed to enumerate all possible junction combinations. (4) Available experimental data are applied as constraints to refine the topology candidates. (5) 3D models based on the topology candidates are developed using computational programs. (6) MD simulations are performed to arrive at (7) potential 3D structure.