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mfold -predition with folding temp from dinamelt

Posted: Thu Jan 26, 2023 2:40 pm
by avivleemann
there is a option to get this result throw mfold unix software?
if to run dinamelt option throw folding I need another unix version I also would like to now which one ?
i ran a sequence throw dinamelt web server quikfold and I want to get the same structure or option of result

The DINAMelt Web Server

Job Parameters
Submitted at Wed 25 Jan 2023 08:21:33 AM UTC

DNA at 25°C
[Na+] = 0.05 M, [Mg++] = 0 M (oligo mode)

Computation took 0.0 seconds.
Sequence 1 ΔG = +2.15 ΔH = +1.30 ΔS = -2.85 Tm = -729.3°C Image: PNG PDF Thermodynamic details
Sequence 1 ΔG = +2.15 ΔH = +5.20 ΔS = +10.23 Tm = 235.2°C Image: PNG PDF Thermodynamic details
Sequence 1 ΔG = +2.51 ΔH = -4.00 ΔS = -21.83 Tm = -89.9°C Image: PNG PDF Thermodynamic details
Sequence 1 ΔG = +2.53 ΔH = -3.40 ΔS = -19.89 Tm = -102.2°C Image: PNG PDF Thermodynamic details
Sequence 1 ΔG = +2.55 ΔH = -1.70 ΔS = -14.25 Tm = -153.9°C Image: PNG PDF Thermodynamic details
Sequence 1 ΔG = +2.75 ΔH = +0.20 ΔS = -8.55 Tm = -296.5°C Image: PNG PDF Thermodynamic details
Sequence 1 ΔG = +2.75 ΔH = -3.00 ΔS = -19.29 Tm = -117.6°C Image: PNG PDF Thermodynamic details
Sequence 1 ΔG = +2.98 ΔH = +2.00 ΔS = -3.29 Tm = -881.1°C Image: PNG PDF Thermodynamic details




thanks aviv

Re: mfold -predition with folding temp from dinamelt

Posted: Mon Jan 30, 2023 7:47 pm
by nmarkham
The Quikfold server at http://www.unafold.org/Dinamelt/applica ... ckfold.php is powered by UNAFold rather than mfold, and we generally steer new users to UNAFold for a handful of reasons.

However, I know it is possible to generate this kind of output from mfold, because Quikfold was powered by mfold at one point. What I don't know for sure is how. I hope Michael can provide specifics.

Basically, you would have to use a tool called "efn" or "efn2" to evaluate the enthalpy of each structure in the .ct file. You could then solve "ΔG = ΔH - TΔS" to get the entropy, and Tm would be the ratio of ΔH divided by ΔS. I don't think there is a single script or command to handle this, but you might be able to write something for your needs. Again, I hope Michael can provide a clearer answer.

By the way, the positive values for ΔG and nonsense values for Tm in your example suggest that that sequence cannot really fold.

Re: mfold -predition with folding temp from dinamelt

Posted: Wed Feb 01, 2023 2:57 pm
by avivleemann
Thank you for the detailed response, much appreciated =]