InterfaceAnalyzer dSasa calculation

[Anonymous]

Hi,

I had previously run InterfaceAnalyzer in Rosetta 3.5 but then had to re-run it with a more recent version (2015.19.57819) and was surprised to notice that the dSASA numbers were quite a bit different. This is not a calculation I expected to change much and it shouldn’t depend on scoring functions.

I just ran the following on 1brs in the integration tests folder:

~/rosetta/rosetta-3.5/rosetta_source/bin/InterfaceAnalyzer.linuxgccrelease -database ~/rosetta/rosetta-3.5/rosetta_database/ @options -run:constant_seed

and

~/rosetta/rosetta_src_2015.19.57819_bundle/main/source/bin/InterfaceAnalyzer.linuxgccrelease -database ~/rosetta/rosetta_src_2015.19.57819_bundle/main/database @options -run:constant_seed

using the options file that came with the 2015.19.57819 test.

Here are the results:

3.5

SCORE: total_score complex_normalized dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA_int dSASA_polar delta_unsatHbonds hbond_E_fraction nres_all nres_int packstat per_residue_energy_int sc_value side1_normalized side1_score side2_normalized side2_score description

SCORE: 0.000 -0.303 -24.366 -1.531 -26.156 -1.643 968.029 1591.537 623.509 5.000 0.448 193.000 66.000 0.000 1.271 0.720 0.555 59.388 -0.003 -0.294 1brs_0001

2015.19.57819

SCORE: total_score complex_normalized dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA_int dSASA_polar delta_unsatHbonds hbond_E_fraction nres_all nres_int packstat per_residue_energy_int sc_value side1_normalized side1_score side2_normalized side2_score description

SCORE: 0.000 0.475 -32.385 -2.055 -34.386 -2.182 794.743 1576.138 781.395 5.000 0.343 193.000 66.000 0.000 1.804 0.720 3.334 123.343 -0.147 -4.265 1brs_0001

All the SASA numbers are quite different:

<blockquote>

                                             3.5     2015.19.57819

dSASA_hphobic    968.029                  794.743

dSASA_int             1591.537                1576.138

dSASA_polar          623.509                   781.395

</blockquote>

Should I just assume that the recent version is more correct?

Thanks much

[Anonymous]

Yes, there have been changes to the SASA calculation since Rosetta 3.5. In particular, the radii of atoms have been changed (reduced) in early 2014. Testing indicates this gives better results, so I would suggest going with the newer values, if you have a choice.

[Anonymous]

Hi,

Rocco is correct. The SASA radii have changed since 3.5 to be more correct. Previously, they were using a set that was parameterized for a no-longer-in-use score function. That said, the changes are relatively minute. Rosetta now uses the radii from reduce by default (see options attached for original references to this radii set). You can now change both the radii set that is used and whether hydrogens are considered implicitly or explicitly. Also note that currently the only method is the LeGrand sasa method, which does not calculate the exact SASA. Most methods do not calculate the exact SASA for speed.

Ok, now, as for the hSASA. Polar atoms were included in the calculation before. If the atoms are polar, why should they be included in the hSASA calculation? This should also be more correct, but it depends on what you think the hSASA should be. There is very little systematic analysis of this number that I’m aware of. The default is to exclude the atom from hSASA if the charge on it is greater than .4 which in terms of protein only means to exclude carbonyl and carboxyl carbons as these are polar. Again, you can change this via an option. These options are now in the SASA option namespace. I list them all here, but I will update the InterfaceAnalyzer docs to reflect these options and changes in a better format shortly (this is the raw format as you can probably tell).

The options are attached in a file to preserve formatting since the forum eats tabs and spaces, unfortunately. I’ll see if it is possible yet to not have that happen. Its python-formated, but the forum does not allow .py files.

Hope this helps!

-Jared

[Author]

Posts