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. Author manuscript; available in PMC: 2008 Aug 31.
Published in final edited form as: J Mol Biol. 2007 Jun 9;371(5):1405–1419. doi: 10.1016/j.jmb.2007.06.003

Table 1.

MD simulations performed

Free Protein Simulation Length Portion of Simulation Selected for Analysis # Snapshots for MM-PB(GB)SA/NMode Analysis
Wild type U1A (closed) 5 ns 2 − 5 ns 150/150
F56A U1A (closed) 5 ns 3 − 5 ns 100/100
F56L U1A (closed) 5 ns 2 − 5 ns 150/150
F56W U1A (closed) 5 ns 2 − 5 ns 150/150
Wild type U1A (open) 5 ns 3 − 5 ns 100/100
F56A U1A (open) 3 ns 0.5 − 3 ns 125/125
F56L U1A (open) 3 ns 0.5 − 3 ns 125/125
F56W U1A (open) 3 ns 0.5 − 3 ns 125/125
Free RNA
Stem loop 2 RNA 32 ns 8 − 32 ns 1200/120
Protein-RNA Complex
Wild type U1A-RNA 3 ns 0.5 − 3 ns 125/125
F56A U1A-RNA 3 ns 0.5 − 3 ns 125/125
F56L U1A-RNA 3 ns 0.5 − 3 ns 125/125
F56W U1A-RNA 3 ns 0.5 − 3 ns 125/125