JamesSweetJones / abYdraw

Input expressions of antibodies in AbML format and output drawings of their shape
GNU General Public License v3.0
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A new one that won't render #61

Open AndrewCRMartin opened 2 months ago

AndrewCRMartin commented 2 months ago
VH.ab(1:8)-CH1(2:9){1}-H(3:17){2}-CH2(4:18)-CH3(5:19)|VL.ab(6:15)-CL(7:16){1}|VL.ab(8:1)-CL(9:2){1}|VH.c(10:12)-CL(11:13)|VL.c(12:10)-CH1(13:11)-L(14)-VH.ab(15:6)-CH1(16:7){1}-H(17:3){2}-CH2(18:4)-CH3(19:5)

So it's a normal IgG (with dual-specificity) with a domain-exchanged Fab (with a third specificity) added to the N-terminus of the heavy chain.

I drew it in exactly that way. Started with an IgG and made both sides specificity ab. Then added the domain swapped Fab (specificity c). This generated the AbML fine, but wouldn't render.

AndrewCRMartin commented 2 months ago

After completing the annotation for this one, it's actually more complex as there is an additional disulphide between the two CH1 domains in the main IgG as well as +/- charges, no sugars and KIH:

VH.ab(1:8)-CH1*_(2:9,15){1,1}-H(3:16){2}-CH2*!(4:17)-CH3*@(5:18){1}|
VL.ab(6:14)-CL+(7:15){1}|
VL.ab(8:1)-CL+(9:2){1}|
VL.c(10:19)-L(11)-CH1*(12:20)-L(13)-VH.ab(14:6)-CH1*_(15:2,7){1,1}-H(16:3){2}-CH2*!(17:4)-CH3*>(18:5){1}|
VH.c(19:10)-CL(20:12)

Good luck!

AndrewCRMartin commented 2 months ago

This one is related:

VH.a(1:3)-CH1(2:4)|
VL.a(3:1)-CL(4:2)-L(5)-VH.b(6:11)-CH1(7:12)-H(8:20)-CH2(9:21)-CH3(10:22)|
VL.b(11:6)-CL(12:7)|
VH.a(13:15)-CH1(14:16)|
VL.a(15:13)-CL(16:14)-L(17)-VH.b(18:23)-CH1(19:24)-H(20:8)-CH2(21:9)-CH3(22:10)|
VL.b(23:18)-CL(24:19)