Globularity [message #1262] |
Wed, 24 March 2021 02:53 ![Go to next message Go to next message](/forum/theme/myThemeWithHFCSS/images/down.png) |
P_Fitz
Messages: 17 Registered: November 2019
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Junior Member |
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I'm dabbling a bit in chemoinformatics and was wondering how a globularity score (specifically as referred to by eNTRy rules https://www.nature.com/articles/nature22308.pdf compares to the Shape Index that is calculated in data warrior.
Thanks so much for developing and supporting such a great tool for free. I've found it very useful in my research.
Patrick Fitzgerald
[Updated on: Wed, 24 March 2021 02:55] Report message to a moderator
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Re: Globularity [message #1266 is a reply to message #1264] |
Fri, 26 March 2021 17:13 ![Go to previous message Go to previous message](/forum/theme/myThemeWithHFCSS/images/up.png) ![Go to next message Go to next message](/forum/theme/myThemeWithHFCSS/images/down.png) |
thomas
Messages: 693 Registered: June 2014
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Senior Member |
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Hi Patrick again,
I just deployed an update, because the recent version was based on the singular values and created too small globularity values. Strangely, the Nature dataset's globularity values also seem too small. Now my calculation uses a singular value decomposition to determine the three orthogonal axes through the molecule that represent largest, second largest and smallest variance of the atom coordinates. Then, I determine along the axes the size of the molecule and divide the smallest by the largest size resulting in a reasonable globularity value. I average individual values of up to 32 random conformers, which were not minimized, but produced with a bias for low energy. The correlation with the 'glob' values of the Nature dataset is smaller than before, but if you explore conformers, create surfaces and visually inspect the molecules, it makes much more sense. One more thing to mention is that the conformers contain all hydrogen atoms, which gives on average slightly larger values than without hydrogens.
Thomas
[Updated on: Fri, 26 March 2021 17:16] Report message to a moderator
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Re: Globularity [message #1268 is a reply to message #1267] |
Tue, 30 March 2021 17:10 ![Go to previous message Go to previous message](/forum/theme/myThemeWithHFCSS/images/up.png) |
thomas
Messages: 693 Registered: June 2014
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Senior Member |
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I made another update with another method to calculate globularity based on the volume and area of the solvent excluded surface (Van der Waals surface). The globularity is the surface of a perfect sphere, whose volume exactly matches the molecule's volume, divided by the real surface of the molecule. In my opinion this is the most reasonable globularity calculation. I also added some documentation and explanation.
Thomas
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