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After modelling, the chosen "best" model for a human SDHB is SDHB_best_model.pdb.
This 3D homology model was carried out using the Modeller software of www.salilab.org/modeller. It follows the advanced tutorial on the Modeller website.
Human SDHB protein NP_002991 is the sequence to be homology modelled onto a 3D structure.
Find existing 3D homologous templates for this protein
2H88:B is a 3D xray crystallography structure of a eukaryote mitochondrial SHDB.
Salilab DBAli was interrogated (here is the command) to list PDB 3D structures similar to 2H88:B.
# Chain A Chain B RMSD(A) SeqId(%)EqPos P-value Res.(A) Name 1 2h88B 8-245 2h88:B 8-245 0.00 100.00 239 29.567 1.74 Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution 2 2h88B 8-245 2h88:O 8-245 0.10 100.00 239 29.567 1.74 Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution 3 2h88B 8-245 2fbw:B 8-245 0.24 100.00 239 29.567 2.10 Avian respiratory complex II with carboxin bound 4 2h88B 8-245 2fbw:O 8-245 0.26 100.00 239 29.567 2.10 Avian respiratory complex II with carboxin bound 5 2h88B 8-245 2h89:B 8-245 0.41 100.00 239 29.567 2.40 Avian Respiratory Complex II with Malonate Bound 6 2h88B 8-245 1yq3:B 8-245 0.43 100.00 239 29.567 2.20 Avian respiratory complex ii with oxaloacetate and ubiquinone 7 2h88B 8-245 1yq4:B 8-245 0.48 100.00 239 29.567 2.33 Avian respiratory complex ii with 3-nitropropionate and ubiquinone 8 2h88B 9-245 1zp0:B 9-245 0.42 89.87 238 29.337 3.50 Crystal Structure of Mitochondrial Respiratory Complex II bound with 3-nitropropionate and 2-thenoyltrifluoroacetone 9 2h88B 9-245 1zoy:B 9-245 0.42 89.87 238 29.337 2.40 Crystal Structure of Mitochondrial Respiratory Complex II from porcine heart at 2.4 Angstroms 10 2h88B 8-245 2bs4:B 1-238 2.18 28.39 237 29.109 2.76 GLU C180 -> ILE VARIANT QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 11 2h88B 8-245 2bs4:E 1-238 2.18 28.39 237 29.109 2.76 GLU C180 -> ILE VARIANT QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 12 2h88B 8-245 1qla:B 1-238 2.23 28.39 237 29.109 ENTRY 2BS2 SUPERSEDES 1QLA 13 2h88B 8-245 1qla:E 1-238 2.23 28.39 237 29.109 ENTRY 2BS2 SUPERSEDES 1QLA 14 2h88B 8-245 1qlb:B 1-238 2.25 28.39 237 29.109 2.33 RESPIRATORY COMPLEX II-LIKE FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 15 2h88B 8-245 1qlb:E 1-238 2.25 28.39 237 29.109 2.33 RESPIRATORY COMPLEX II-LIKE FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 16 2h88B 8-245 2bs2:E 1-238 2.19 27.97 237 29.109 1.78 QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 17 2h88B 8-245 2bs2:B 1-238 2.22 27.97 237 29.109 1.78 QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 18 2h88B 8-245 2bs3:B 1-237 2.23 27.97 237 29.109 2.19 GLU C180 -> GLN VARIANT QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 19 2h88B 8-245 2bs3:E 1-237 2.23 27.97 237 29.109 2.19 GLU C180 -> GLN VARIANT QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 20 2h88B 9-245 1e7p:B 2-238 2.20 28.51 236 28.974 3.10 QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 21 2h88B 9-245 1e7p:E 2-238 2.20 28.51 236 28.974 3.10 QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 22 2h88B 9-245 1e7p:H 2-238 2.20 28.51 236 28.974 3.10 QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 23 2h88B 9-245 1e7p:K 2-238 2.20 28.51 236 28.974 3.10 QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES 24 2h88B 10-245 1nek:B 1-236 2.39 50.21 234 28.556 2.60 Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound 25 2h88B 10-245 1nen:B 1-236 2.40 50.21 234 28.556 2.90 Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site 26 2h88B 10-245 2acz:B 1-236 2.37 50.43 233 28.422 3.10 Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site 27 2h88B 8-245 1fum:N 2-234 1.99 28.88 233 28.292 ENTRY 1L0V SUPERSEDES 1FUM 28 2h88B 8-245 1fum:B 2-234 2.02 30.30 232 28.066 ENTRY 1L0V SUPERSEDES 1FUM 29 2h88B 8-245 1l0v:N 2-234 2.02 30.30 232 28.066 3.30 Quinol-Fumarate Reductase with Menaquinol Molecules 30 2h88B 8-245 1kf6:B 2-234 2.03 30.30 232 28.066 2.70 E. coli Quinol-Fumarate Reductase with Bound Inhibitor HQNO 31 2h88B 8-245 1kfy:B 2-234 2.04 30.30 232 28.066 3.60 QUINOL-FUMARATE REDUCTASE WITH QUINOL INHIBITOR 2-[1-(4-CHLORO-PHENYL)-ETHYL]-4,6-DINITRO-PHENOL 32 2h88B 8-245 1l0v:B 2-234 1.95 30.43 231 27.933 3.30 Quinol-Fumarate Reductase with Menaquinol Molecules 33 2h88B 8-245 1kf6:N 2-234 1.96 30.43 231 27.933 2.70 E. coli Quinol-Fumarate Reductase with Bound Inhibitor HQNO 34 2h88B 8-245 1kfy:N 2-234 1.96 30.43 231 27.933 3.60 QUINOL-FUMARATE REDUCTASE WITH QUINOL INHIBITOR 2-[1-(4-CHLORO-PHENYL)-ETHYL]-4,6-DINITRO-PHENOL 35 2h88B 8-245 2b76:N 2-234 2.38 28.38 230 27.800 3.30 E. coli Quinol fumarate reductase FrdA E49Q mutation 36 2h88B 8-245 2b76:B 2-234 2.37 28.38 230 27.708 3.30 E. coli Quinol fumarate reductase FrdA E49Q mutation Align the existing 3D templates into separate '*_fit.pdb' models to each other, and produce a 2D sequence alignment for the sequences of 3D templates
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_salign.py > sdhb_salign.log ---> sdhb_salign.ali, sdhb_salign.pap grep '_E>' salign_sdhb.log grep '_W>' salign_sdhb.log pymol 2H88B_fit.pdb 2H88O_fit.pdb 2FBWB_fit.pdb 2FBWO_fit.pdb 2H89B_fit.pdb 1YQ3B_fit.pdb 1YQ4B_fit.pdb 1ZP0B_fit.pdb 1ZOYB_fit.pdb 2BS4B_fit.pdb 2BS4E_fit.pdb 1QLBB_fit.pdb 1QLBE_fit.pdb 2BS2B_fit.pdb 2BS2E_fit.pdb 2BS3B_fit.pdb 2BS3E_fit.pdb 1E7PB_fit.pdb 1E7PE_fit.pdb 1E7PH_fit.pdb 1E7PK_fit.pdb 1NEKB_fit.pdb 1NENB_fit.pdb 2ACZB_fit.pdb 1L0VB_fit.pdb 1L0VN_fit.pdb 1KF6B_fit.pdb 1KF6N_fit.pdb 1KFYB_fit.pdb 1KFYN_fit.pdb 2B76B_fit.pdb 2B76N_fit.pdb ---> SDHB_superpose_all_xrays.pngAlign the 2D sequences between the 3D templates and the 2D sequence for which a 3D homology model will be created further on using the 3D templates
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_align2d_mult.py > sdhb_align2d_mult.log ---> NP_002991_mult.ali, NP_002991_mult.pap Create ten difference 3D homology models for the 2D sequence
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_model_mult.py > sdhb_model_mult.log ---> NP_002991.B99990001.pdb, NP_002991.B99990002.db, ... NP_002991.B99990010.db Calculate the DOPE energy score for each of the 3D templates
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2H88B.py > sdhb_evaluate_model_2H88B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2H88O.py > sdhb_evaluate_model_2H88O.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2FBWB.py > sdhb_evaluate_model_2FBWB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2FBWO.py > sdhb_evaluate_model_2FBWO.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2H89B.py > sdhb_evaluate_model_2H89B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1YQ3B.py > sdhb_evaluate_model_1YQ3B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1YQ4B.py > sdhb_evaluate_model_1YQ4B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1ZP0B.py > sdhb_evaluate_model_1ZP0B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1ZOYB.py > sdhb_evaluate_model_1ZOYB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2BS4B.py > sdhb_evaluate_model_2BS4B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2BS4E.py > sdhb_evaluate_model_2BS4E.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1QLBB.py > sdhb_evaluate_model_1QLBB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1QLBE.py > sdhb_evaluate_model_1QLBE.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2BS2B.py > sdhb_evaluate_model_2BS2B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2BS2E.py > sdhb_evaluate_model_2BS2E.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1E7PB.py > sdhb_evaluate_model_1E7PB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1E7PE.py > sdhb_evaluate_model_1E7PE.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1E7PH.py > sdhb_evaluate_model_1E7PH.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1E7PK.py > sdhb_evaluate_model_1E7PK.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1NEKB.py > sdhb_evaluate_model_1NEKB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1NENB.py > sdhb_evaluate_model_1NENB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2ACZB.py > sdhb_evaluate_model_2ACZB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1L0VB.py > sdhb_evaluate_model_1L0VB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1L0VN.py > sdhb_evaluate_model_1L0VN.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1KF6B.py > sdhb_evaluate_model_1KF6B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1KF6N.py > sdhb_evaluate_model_1KF6N.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1KFYB.py > sdhb_evaluate_model_1KFYB.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_1KFYN.py > sdhb_evaluate_model_1KFYN.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2B76B.py > sdhb_evaluate_model_2B76B.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_2B76N.py > sdhb_evaluate_model_2B76N.log ---> 2H88B.profile, 2H88O.profile, 2FBWB.profile, 2FBWO.profile, etc. Calculate the DOPE energy score (a type of force field made up of distance constrainsts and some elements of the CHARMM force field) for each of the ten generated 3D homology models
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990001.py > sdhb_evaluate_model_NP_002991_B99990001.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990002.py > sdhb_evaluate_model_NP_002991_B99990002.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990003.py > sdhb_evaluate_model_NP_002991_B99990003.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990004.py > sdhb_evaluate_model_NP_002991_B99990004.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990005.py > sdhb_evaluate_model_NP_002991_B99990005.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990006.py > sdhb_evaluate_model_NP_002991_B99990006.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990007.py > sdhb_evaluate_model_NP_002991_B99990007.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990008.py > sdhb_evaluate_model_NP_002991_B99990008.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990009.py > sdhb_evaluate_model_NP_002991_B99990009.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_evaluate_model_NP_002991_B99990010.py > sdhb_evaluate_model_NP_002991_B99990010.log ---> NP_002991.B99990001.profile, NP_002991.B99990002.profile, ... NP_002991.B99990010.profile grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990001.log DOPE score : -26757.222656 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990002.log DOPE score : -27105.140625 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990003.log DOPE score : -26660.478516 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990004.log DOPE score : -26653.312500 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990005.log DOPE score : -26810.972656 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990006.log DOPE score : -26434.369141 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990007.log DOPE score : -26881.345703 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990008.log DOPE score : -26136.630859 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990009.log DOPE score : -26607.103516 grep 'DOPE score' sdhb_evaluate_model_NP_002991_B99990010.log DOPE score : -26827.523438 Visually compare the DOPE energy functions of the ten generated 3D homology models and a couple of the 3D templates
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_plot_profiles_NP_002991_B99990001_to_B99990010_2H88B_2FBWB.py> ---> dope_profile_NP_002991_B99990001_to_B99990010_2H88B_2FBWB_loc1.pngChoose the best 3D homology model (B99990005) to continue trying to refine it Choose by the lowest DOPE score and by a visual DOPE energy function that closely follows the DOPE energy function of the 3D templates
The DOPE energy function graph plot shows that the 3D homology models do not closely follow the 3D templates in the region of residues 170-190
Run the loop modelling function (a type of molecular-dynamics/conformational search) to try to find betters models for residues 170-190 only for the chosen 3D homology model B99990005
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_loop_refine.py > sdhb_loop_refine.log ---> NP_002991.BL00010001.pdb, NP_002991.BL00020001.pdb, ... NP_002991.BL05000001.pdb Calculate the DOPE energy score (a type of force field made up of distance constrainsts and some elements of the CHARMM force field) for each of the 500 loop modelling refinement models
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_model_energies.py > sdhb_model_energies.log egrep 'DOPE score|openf___224_> Open NP' sdhb_model_energies.log > sdhb_dope_scores_for_500_loop_models.txt Graph plot the DOPE energy score for each of the 500 loop modelling refinement models
/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_generate_multiple_plot_graphs.py ---> dope_multiple_plot_NP_002991_BL00010001_to_BL00100001_2H88B.png .. dope_multiple_plot_NP_002991_BL04910001_to_BL05000001_2H88B.png /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_plot_some_of_many_tries_1.py /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_plot_some_of_many_tries_2.py /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_plot_some_of_many_tries_3.py /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_plot_some_of_many_tries_4.py
Visually inspect the graph plots of the DOPE energy scores for each of the 500 loop modelling refinement models Choose the one that most closely follows the 3D template for residues 170-190 - BL04060001
cp NP_002991.BL04060001.pdb SDHB_NP_002991_model.pdb cp NP_002991.BL04060001.profile SDHB_NP_002991_model.profile /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_plot_NP_002991_model.py ---> dope_profile_sdhb_NP_002991_model.pngFill in the chain-id in the 3D homology models created by Modeller Copy the chosen models to generic names for easy future reference
Compare the 3D homology models to a previous model created in the Discovery Studio version of Modeller that was on the Windows platform
perl -T renamepdbchain.pl -infile SDHB_NP_002991_model.pdb -tochain B mv SDHB_NP_002991_model.pdb.pdb SDHB_model.pdb cp SDHB_NP_002991_model.profile SDHB_model.profile cat SDHB_header.pdb SDHB_model.pdb > SDHB_model_with_header.pdb perl -T renamepdbchain.pl -infile NP_002991.B99990005.pdb -tochain B cp NP_002991.B99990005.profile SDHB_first_model.profile mv NP_002991.B99990005.pdb.pdb SDHB_first_model.pdb cat SDHB_header.pdb SDHB_first_model.pdb > SDHB_first_model_with_header.pdb mv SDHB_first_model_with_header.pdb SDHB_first_model.pdb cat SDHB_header.pdb SDHB_previous_model.pdb > SDHB_previous_model_with_header.pdb mv SDHB_previous_model_with_header.pdb SDHB_previous_model.pdb /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_superpose_models.py > sdhb_superpose_models.log pymol SDHB_model_fit.pdb SDHB_first_model_fit.pdb SDHB_previous_model_fit.pdb 2H88_fit.pdb ---> SDHB_superpose_models.png/home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_3d_align_some_models.py > sdhb_3d_align_some_models.log /home/emma/bin/modeller9v8/bin/modpy.sh python sdhb_plot_model_dope_energies.py ---> sdhb_plot_model_dope_energies.png
cp SDHB_model.pdb SDHB_last_model.pdb cp SDHB_model.profile SDHB_last_model.profile cp SDHB_first_model.pdb SDHB_best_model.pdb cp SDHB_first_model.profile SDHB_best_model.profile A visual inspection, using PyMOL, shows that the loop-modelling-refined 3D model has lost secondary structure (ie. alpha-helix) at residues 170-190, whereas all 3D templates do have this alpha-helix there So choose the best 3D model that was found before loop-modeling refinements, because it has the alpha-helix at residues 170-190 This means that the results of the loop-modelling have not been chosen
