Homology modelling Gaucher Disease

Template selection

<figtable id="tab:ss_mapping">

Hit Nr	Template	Identity	HHsearch prob
> 80% sequence identity
1	2nt0_A	100.0	100.0
40% - 80% sequence identity
< 30% sequence identity
2	2wnw_A	28.0	100.0
3	3clw_A	14.0	100.0
4	2y24_A	18.0	100.0
5	3kl0_A	19.0	100.0
6	3zr5_A	17.0	100.0
7	3ik2_A	14.0	99.2
22	3nco_A	11.0	97.7
28	1egz_A	12.0	97.4

</figtable>

Modeller

Single-template modeling

2wnw_A

2y24_A

3nco_A

<figure id="fig:modeller-single-dope">

Dope score per residue.

</figure>

<figtable id="tab:modeller_results">

Template	DOPE	DOPE z-score	QMEAN6	RMSD	TM-score	GDT_TS	GTD_HA
2wnw_A	-55925	-0.471	0.689	1.006	0.824	0.661	0.479
2y24_A	-47194	0.777	0.376	1.222	0.550	0.294	0.223
3nco_A	-44033	1.224	0.139	2.158	0.252	0.093	0.043

</figtable>

Multiple-template modeling

2wnw_A-2y24_A-3kl0_A

2wnw_A-3nco_A

3ik2_A-3nco_A-1egz_A

<figtable id="tab:modeller_results">

Template	DOPE	DOPE z-score	QMEAN6	RMSD	TM-score	GDT_TS	GTD_HA
2wnw_A-2y24_A-3kl0	-39084	1.930	0.314	1.987	0.465	0.277	0.179
2wnw_A-3nco_A	-46962	0.807	0.556	1.256	0.778	0.593	0.409
3ik2_A-3nco_A-1egz_A	-25391	0.3881	0.101	6.607	0.241	0.062	0.029

</figtable>

SWISS-MODEL

Automated mode

2wnw_A

2y24_A

3nco_A

<figtable id="tab:modeller_results">

Template	DOPE	DOPE z-score	QMEAN6	RMSD	TM-score	GDT_TS	GTD_HA
2wnw_A	-53863	-0.786	0.530	1.003	0.858	0.723	0.540
2y24_A	-42674	0.565	0.430	1.100	0.712	0.539	0.382
3nco_A	-27101	2.109	0.270	2.158	0.422	0.252	0.138

</figtable>

Alignment mode

2wnw_A

2y24_A

3nco_A

<figtable id="tab:modeller_results">

Template	DOPE	DOPE z-score	QMEAN6	RMSD	TM-score	GDT_TS	GTD_HA
2wnw_A	-53963	-0.788	0.540	1.011	0.859	0.722	0.536
2y24_A	-40131	1.055	0.360	1.222	0.510	0.238	0.067
3nco_A	-30244	0.689	0.240	2.001	0.426	0.247	0.135

</figtable>