RNADraw

[westerm at aclcb.purdue.edu]

>Patrick O'Neil <patrick at corona> has questions about RNADraw:

While I've just started exploring this program and thus am not an authority on 
it, it does seem to me that it is calculating your simple structure correctly 
and that, somewhere, you are mistaken in your hand calculations. Note, however, 
that the program seems to be reporting KJ instead of KCal; e.g., when it says 
'-3.6 KJ' it really should be '-3.6 KCal'. 

For your structure, the program (and MFold by Zuker and a homegrown 
program by us) calculates the best structure with -3.6 KCal as:

>				 A
>  5'-C C G U A U U U G G C C G G   A
>		      3'-G G C C   U
>				 A
>
A breakout of the structure's energy is:

      Left Arm  Right Arm    Length             ............ Energy ...........
Stem    5'   3'   5'   3'  Stem Loop  Loop type   stem dngle  loop dngle    net
----  ---- ---- ---- ----  ---- ----  --------- ------ ----- ----- ----- ------
   1    11   14   19   22     4    4    hairpin   -7.8  -0.2   5.5  -1.1   -3.6


Somehow you hand calculated this as -2.1 KCal.

Your proposed 'best' structure:

>		       G G	
>   5'- C C G U A U U U     C
>   3'- G G C A U A A G
>          C            G C 

Which your hand calculation, Mfold, and my program all give as -3.2 KCal. 

The breakout of this:

      Left Arm  Right Arm    Length             ............ Energy ...........
Stem    5'   3'   5'   3'  Stem Loop  Loop type   stem dngle  loop dngle    net
----  ---- ---- ---- ----  ---- ----  --------- ------ ----- ----- ----- ------
   1     1    2   21   22     2    1      bulge   -2.9   0.0   3.9  -2.0   -1.0
   2     3    8   14   19     6    5    hairpin   -5.5   0.0   4.9  -1.6   -2.2


The RNAdraw program calculates this structure as -1.2 KCal. I suspect it is 
leaving off the terminal stacking energies (i.e., 'dngle' -- dangle energies)  
in stem #1.