. Author manuscript; available in PMC: 2014 Sep 20.

Published in final edited form as: J Comput Aided Mol Des. 2010 Sep 30;24(11):943–956. doi: 10.1007/s10822-010-9386-9

Table 3.

Averages and standard deviations of the interaction energy (kcal/mol) of the complex

No	SHP_DAX-1		SHP_USP		SHP_RXR_α		SHP_RXR_α*
	Energy	RMSD	Energy	RMSD	Energy	RMSD	Energy	RMSD
	Average	Average	Average	Average	Average	Average	Average	Average
	SD	SD	SD	SD	SD	SD	SD	SD
2	−145.962	4.734	−151.591	3.998	−117.696	2.820	−118.340	2.619
	±28.394	±0.431	±21.721	±0.483	±28.197	±0.430	±13.021	±0.286
	/	/	−108.364	3.902	−111.411	4.129	−43.405	4.014
			±11.195	±0.465	±33.811	±0.607	±13.254	±0.846
3	−138.822	2.252	−135.318	4.182	−65.691	4.029	−50.503	3.839
	±14.885	±0.425	±19.109	±0.369	±20.397	±0.542	±12.881	±0.418
	/	/	−194.395	3.151	−39.512	3.986	−69.928	2.674
			±25.340	±0.499	±11.607	±0.460	±9.655	±0.463
4	−141.538	4.362	−157.385	3.677	−82.558	3.760	−10.556	3.716
	±24.897	±0.403	±22.642	±0.378	±27.442	±0.241	±14.510	±1.143
	/	/	−127.603	4.672	−10.448	4.719	/	/
			±28.081	±0.595	±11.739	±0.552

Averages and standard deviations of the RMSD (Å) calculated using the heavy atoms of the ligand and the binding pose obtained from docking experiments as reference structure. All the values are calculated along the last 8 ns of the MD simulations. Selected solutions are highlighted in italic