Copyright Mirela Andronescu and David H. Mathews 2005-2007 http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1998/37/i42/pdf/bi9809425.pdf Copied from acroread, removed the slashes and the p's Experiments from other papers were included here The Non-Two-State Sequences are not included. There is plenty of canonical pair data available without the two state data. (communication with Dave Mathews)

http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i40/pdf/bi026201s.pdf Copied from acroread

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1998/37/i45/pdf/bi981732v.pdf I did not include these values (the NaCl concentration is 100mM, instead of 1M, as in the other cases), because the change in salt concentration changes the stability. (communication with Dave Mathews)

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1997/36/i16/pdf/bi962608j.pdf The pdf file has tables as pictures, so they can't be copied. Took data from Zhi Lu's table, added second digit precision and STD

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1998/37/i04/pdf/bi972050v.pdf The pdf file has tables as pictures, so they can't be copied. Took data from Zhi Lu's table, added second digit precision and STD

These are considered hairpin loop terminal mismatches in the paper. I don't know the ERR-dG-37, I just put 5%.

http://www.rnajournal.org/cgi/reprint/6/4/608.pdf Copied from acroread Did not include Table 4B (communication with Dave Mathews).

These are considered hairpin loop terminal mismatches in the paper. It's not clear what is the experimental error for the duplexes. 5% sounds reasonable (communication with Dave Mathews).

http://nar.oxfordjournals.org/cgi/content/abstract/20/4/819 Copied from acroread STD-dG-37 0.3 sounds more conservative than 0.2 (communication with Dave Mathews).

http://nar.oxfordjournals.org/cgi/content/abstract/19/21/5901 Some of the data in Table 1 are the same as Table 1 from Antao_Tinoco_1992, however the values are different. I included them, and the parser should be aware that there can be duplicates with which it should take the average (communication with Dave Mathews). In fact, I'm doing regression, so I don't think the parser needs to know anything.

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1994/33/i47/pdf/bi00251a042.pdf I've also included Table 3 as motif stem (communication with Dave Mathews). Copied from acroread

These are considered hairpin loop terminal mismatches in the paper. By convention, we use the results from 1/Tm vs log Ct/4 plots, and not the ones from average of curve fits (communication with Dave Mathews).

The pdf file has tables as pictures, so they can't be copied. Took data from Zhi Lu's table, added second digit precision and STD

http://nar.oxfordjournals.org/cgi/content/abstract/21/16/3845 The pdf file has tables as pictures, so they can't be copied. Took data from Zhi Lu's table, added second digit precision and STD It looks like having triphosphate at one end gives different values

http://nar.oxfordjournals.org/cgi/content/abstract/16/24/11725 Took data from Zhi Lu's table, added second digit precision and STD Are the ends dangling ends, or terminal mismatches?

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1986/25/i11/pdf/bi00359a019.pdf No dG values, I computed them from enthalpy and entropy (communication with Dave Mathews). The following are self-complementary (self complementary = a strand can form a duplex with another identical strand - communication with Dave Mathews).

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1989/28/i02/pdf/bi00428a049.pdf Structures written by hand, values copied from acroread Are the ends dangling ends, or terminal mismatches? Error 5% sounds reasonable (communication with Dave Mathews).

http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i33/pdf/bi025781q.pdf Copied from acroread If the bulge can be in more than one place, I added one line per place I put error of 5% on dG-37.

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1990/29/i01/pdf/bi00453a038.pdf Copied from acroread I did not include this table of homoduplexes. Homoduplex is a duplex formed with itself. It is not quite self-complementary because the sequences are very complementary. We skipped this table because it is not obvious as to what these self-structures are (communication with Dave Mathews).

I did not include this table. This was an attempt to analyze the data differently and affected dG very little (communication with Dave Mathews).

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1991/30/i46/pdf/bi00110a015.pdf Copied from acroread All the G-U were considered pairs, except (GGUC)2, which was considered 2x2 internal loop, according to Mathews_Turner_1999. (This may give non-full rank matrix) I did not include the non-two-state transitions. They are not good (communication with Dave Mathews).

http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2001/40/i08/pdf/bi002564l.pdf Copied from acroread Self-complementary means that a strand can form a duplex with another identical strand. Note that this does not require the symmetry penalty unless the structure is symmetric. The following is self-complementary and symmetric (communication with Dave Mathews).

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/2000/39/i31/pdf/bi000229r.pdf The Table is as picture :(, I had to write all the data by hand. The following structure has A-A pair at the end. I think there is a mistake, considering Figure 1. The second one must be a U. the following structure has A-A pair at the end. I think there is a mistake, considering Figure 1. The second one must be a U. The following two are outliers: the error is greater than 1 kcal/mol

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/2000/39/i31/pdf/bi000229r.pdf The Table is as picture :(, I had to write all the data by hand. for the following, we don't have the value for the STD-dG-37. I just put 0.2

http://pubs.acs.org/cgi-bin/sample.cgi/bichaw/2003/42/i48/pdf/bi0301587.pdf Copied from acroread Since The following 3x3, 2x3 etc parameters are not included in my model yet, A lot of the following lines give conflicts. I removed all of them for now.

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1991/30/i26/pdf/bi00240a013.pdf Copied from acroread I don't need the values in parentheses (i.e. parameters corrected for single-strand extinction coefficients). I used the out of parantheses values, to be consistent to the rest of the database (communication with Dave Mathews).

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1996/35/i50/pdf/bi961789m.pdf The Table is as picture :(, I had to write all the data by hand. the following structure has U-U pair at the end. I think there is a mistake, the first one must be an A.

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1995/34/i10/pdf/bi00010a009.pdf Copied from acroread

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1994/33/i37/pdf/bi00203a033.pdf Copied from acroread

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1991/30/i33/pdf/bi00247a021.pdf Copied from acroread

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1997/36/i41/pdf/bi971069v.pdf Copied from acroread All the adjacent G-U were considered pairs, except (GGUC)2, which is considered 2x2 internal loop, according to Mathews_Turner_1999. If only one of the 2 pairs is G-U, and the other is a mismatch (e.g. A-G), the G-U was not considered paired, and the A-G 1x1 mismatch, but all was a 2x2 internal loop.

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1999/38/i43/pdf/bi991186l.pdf Copied from acroread Did not use the non-two-state melting values. This contains a G-U "internal loop", but we consider it to be a base pair.

http://www.dnasoftware.com/Science/Publications/pdf/ja00011a039%20JSL%20JACS1991.pdf Copied from acroread I didn't include the duplexes with modified nucleotides (I, P, 2), because the nearest neighbour model doesn't deal with modified nucleotides. The following two are the same and have different values, because they are from different sources. I included both, and the regression will take care of them.

http://www.pnas.org/cgi/reprint/101/19/7287 Written by hand, from the supporting text

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1996/35/i45/pdf/bi9615710.pdf Copied from acroread All the G-U were considered pairs, except (GGUC)2, which is considered 2x2 internal loop, because they are non-nearest-neighbor, according to Mathews_Turner_1999. (communication with Dave Mathews)

http://nar.oxfordjournals.org/cgi/reprint/27/4/1118 Written by hand, couldn't copy from acroread

http://nar.oxfordjournals.org/cgi/content/abstract/23/2/302 Copied from acroread The following are self-complementary. In general, there is no reason why these need to be symmetric, so I would leave the symmetry penalty off. (communication with Dave Mathews).

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1997/36/i49/pdf/bi9716783.pdf I tried to include Table 2 and 3, but it's not clear to me what those numbers represent exactly (the difference is between what and what?). So for now, they are not included. I skipped this data and only used optical melting data (communication with Dave Mathews). http://pubs.acs.org/cgi-bin/searchRedirect.cgi/bichaw/2004/43/i40/pdf/bi049168d.pdf Copied from acroread

http://pubs.acs.org/cgi-bin/searchRedirect.cgi/bichaw/2005/44/i08/pdf/bi048079y.pdf Copied from acroread At the beginning of every Seq2, there was a P for purine (A or G). I replaced the odd ones with A, and the even ones with G.

http://pubs.acs.org/cgi-bin/searchRedirect.cgi/bichaw/2005/44/i50/pdf/bi051659q.pdf Copied from acroread The values for the following three duplexes are obtained from the best fit of calculated transitions. I included them for now. Is that good?

http://pubs.acs.org/cgi-bin/archive.cgi/bichaw/1986/25/i19/pdf/bi00367a061.pdf dG values are not given. I did not use the temperature-dependent numbers. I calculated DG from DH and DS. The temperature dependent numbers were generated using an alternative method for data analysis. (communication with Dave Mathews) I removed the predicted values, i.e. the ones in parantheses, and with superscript f.

http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2001/40/i23/pdf/bi0029548.pdf Copied from acroread Here, state 0 is not the completely unfolded state, but it's the hairpin formed by sequence0.

http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i03/pdf/bi011441d.pdf Copied from acroread Here, state 0 is not the completely unfolded state, but it's the hairpin formed by sequence0.