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andrabujan / CATH-summer-2019

This repository contains materials related to superfamily naming and renaming
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Fragments as representative domains #4

Open andrabujan opened 5 years ago

andrabujan commented 5 years ago

1.10.10.2630 should be re-classified since the representative domain looks like a fragment; superfamily 3.30.190.20 is mapped to the same Pfam family, which has a better mapping; the representative domain of 1.10.102630 seems to overlap with the representative domains in 3.30.190.20, so perhaps it could also be possible to merge the two superfamilies?

andrabujan commented 5 years ago

2.40.240.120 looks like one of these cases too; it's quite a small superfamily, only 540 sequences

andrabujan commented 5 years ago

2.30.170.40 representative domains look quite unpacked and non-globular. also chopping issue for the third representative domain

andrabujan commented 5 years ago

4.10.950.10 - representative domains look like fragments - not globular, not packed, few secondary structure elements

andrabujan commented 5 years ago

1.10.720.90 - 3D view is not available but the superfamily superposition seems to show a single helix domain; the suggested superfamily name and Pfam overlaps with superfamily 1.10.1900.20

andrabujan commented 5 years ago

1.10.1200.60 - small superfamily, it is a linker - not very packed

kmatwani commented 5 years ago

Non-globular domains: 3.90.20.20 and 1.20.58.880

kmatwani commented 5 years ago

Non globular domain: 2.20.25.480

andrabujan commented 5 years ago

4.10.830.10 - doesn't look very packed and has few secondary structure elements

andrabujan commented 5 years ago

1.20.5.1150 non globular domain and 3D view not available

andrabujan commented 5 years ago

4.10.960.10 - very unpacked, non globular domain; few secondary structures

kmatwani commented 5 years ago

Non-globular domain: 1.20.5.350

kmatwani commented 5 years ago

Non-globular domain: 1.10.1690.10

andrabujan commented 5 years ago

2.30.36.70 doesn't look very packed, few secondary structures; might be a chopping issue (chopped as a separate domain - the full length domain is found in 3.30.420.40)