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[[Fabry Disease]] » [[Fabry:Homology_based_structure_predictions|Homology based structure predictions]] » Journal <hr> == Dataset preparation == The homology search was performed online and resulted in the two output files [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] and [https://www.dropbox.com/s/ycfy8ke6xt3ofrp/coma.out.txt coma.out] for the structure search with [http://toolkit.tuebingen.mpg.de/hhpred HHpred] and [http://bioinformatics.ibt.lt:8085/coma/ COMA], respectively. In both cases, we used the default values, thresholds and databases. From both the resulting files we tried in each case to create three distinct datasets with the demanded sequence identity to the target protein with the following calls and scripts. perl [https://www.dropbox.com/s/8vu2mnnl733f3zh/make_dataset_hhpred.pl.txt make_dataset_hhpred.pl] [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] 0.0000000000000001 This resulted in the HHpred datasets mentioned in [[Fabry:Homology_based_structure_predictions#Dataset_preparation | Dataset preparation]] Table 1 and the corresponding pdb structure files. perl [https://www.dropbox.com/s/vul8gare1lgwgk5/make_dataset_coma.pl.txt make_dataset_coma.pl] [https://www.dropbox.com/s/ycfy8ke6xt3ofrp/coma.out.txt coma.out] 0.002 This resulted in the Coma datasets mentioned in [[Fabry:Homology_based_structure_predictions#Dataset_preparation | Dataset preparation]] Table 2 and the corresponding pdb structure files. == Calculation of models == === Modeller === The following steps resulted in 10 models, which can all be downloaded [https://www.dropbox.com/s/537aoxmswsxrebq/models_Modeller.zip here]. ==== Default settings ==== For the standard homology modeling with Modeller two basic scripts were used, which build up on the ones described in the recommended [[Using_Modeller_for_TASK_4 | tutorial]]: [https://www.dropbox.com/s/un3vvkpn9ig5uzw/1_align.py.txt 1_align.py] and [https://www.dropbox.com/s/p3641etp7ave8rk/2_Single_template_modeling.py.txt 2_Single_template_modeling.py] (in this case example file for 1ktb) which need the appropriate template pdb structure files, as well as the target (AGAL) sequence in pir format as input: >P1;1R46 sequence:1R46:::::::0.00: 0.00 MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEP DSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQL ANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENL ADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIK SILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDL RHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWAVAMINRQEIG GPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENT MQMSLKDLL* The following runs were performed on our home computers: #3HG3 100% mod9.10 1_align_3hg3.py mod9.10 2_Single_template_modeling_3hg3.py #1KTB 53% mod9.10 [https://www.dropbox.com/s/un3vvkpn9ig5uzw/1_align.py.txt 1_align.py] mod9.10 [https://www.dropbox.com/s/p3641etp7ave8rk/2_Single_template_modeling.py.txt 2_Single_template_modeling.py] #3CC1 25% mod9.10 1_align_3cc1.py mod9.10 2_Single_template_modeling_3cc1.py ==== Multiple templates ==== For multiple templates three scripts are needed, which again base on the [[Using_Modeller_for_TASK_4 | tutorial]] and are here again only exemplified for one case: [https://www.dropbox.com/s/llx00q42jiym0zo/3_multiAli_1.py 3_multiAli_1.py], [https://www.dropbox.com/s/mntoiuphufx5fjh/4_add1R46_1.py 4_add1R46_1.py] and [https://www.dropbox.com/s/dz1sgsad1knpe8s/5_multipleMod_1.py 5_multipleMod_1.py] The following combinations were performed: #Multiple 3HG3,1KTB mod9.10 [https://www.dropbox.com/s/llx00q42jiym0zo/3_multiAli_1.py 3_multiAli_1.py] mod9.10 [https://www.dropbox.com/s/mntoiuphufx5fjh/4_add1R46_1.py 4_add1R46_1.py] mod9.10 [https://www.dropbox.com/s/dz1sgsad1knpe8s/5_multipleMod_1.py 5_multipleMod_1.py] #Multiple 3HG3,1KTB,3CC1 mod9.10 3_multiAli_2.py mod9.10 4_add1R46_2.py mod9.10 5_multipleMod_2.py #Multiple 3CC1, 3ZSS, 3A24 mod9.10 3_multiAli_3.py mod9.10 4_add1R46_3.py mod9.10 5_multipleMod_3.py #Multiple 3CC1, 3HG3 mod9.10 3_multiAli_4.py mod9.10 4_add1R46_4.py mod9.10 5_multipleMod_4.py ==== Edited Alignment input ==== For the edited alignment models, only the second Modeller script [https://www.dropbox.com/s/p3641etp7ave8rk/2_Single_template_modeling.py.txt 2_Single_template_modeling.py] was needed. Edited alignments were provided as input. We rearranged them with the program [http://molecularevolution.org/software/alignment/seaview SeaView]. #Active Site shifted right to next D (7 and 1) in -2d.ali mod9.10 2_Single_template_modeling_3hg3_changed_actSite.py #Active Site shifted right to next D (7 and 1) in both ali files mod9.10 2_Single_template_modeling_3hg3_changed_actSite_2.py #Active Site shifted right to next D (7 and 1) in both ali files + Substrate binding region (203-207) forced to be consecutive mod9.10 2_Single_template_modeling_3hg3_changed_actSite_3.py === Swissmodel === === iTasser === === 3D-Jigsaw === == Evaluation == [[Category: Fabry Disease 2012]]

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