Difference between revisions of "CD task7 protocol"
From Bioinformatikpedia
(→FoldX) |
(→FoldX) |
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==FoldX== |
==FoldX== |
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− | + | list.txt |
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− | + | 2O4H.pdb |
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− | + | individual_list.txt |
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+ | EA285A; |
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− | E285A,A305E,G123E,R71H,R71K,K213E,V278M,M82T,E235K,I270T; |
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+ | AA305E; |
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+ | GA123E; |
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+ | RA71H; |
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+ | RA71K; |
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+ | KA213E; |
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+ | VA278M; |
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+ | MA82T; |
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+ | EA235K; |
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+ | IA270T; |
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run.txt |
run.txt |
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<JOBSTART>#; |
<JOBSTART>#; |
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<PDBS>#; |
<PDBS>#; |
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− | <BATCH> |
+ | <BATCH>list.txt; |
<COMMANDS>FOLDX_commandfile; |
<COMMANDS>FOLDX_commandfile; |
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− | <BuildModel>#, |
+ | <BuildModel>#,individual_list.txt; |
<END>#; |
<END>#; |
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<OPTIONS>FOLDX_optionfile; |
<OPTIONS>FOLDX_optionfile; |
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command |
command |
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− | /opt/SS12-Practical/foldx/FoldX.linux64 |
+ | /opt/SS12-Practical/foldx/FoldX.linux64 => choose 3 => run.txt |
Revision as of 20:58, 20 June 2012
Choosing structure
So, we decided to use 2O4H, since it has a bound substrate, low resolution and a listed pH value.
Apo-structure: 2O53 Resolution: 2,7, R-free: 0,269, pH: 6.0, chains: A,B Holo-structure: 2O4H Resolution: 2,7, R-free: 0,271, pH: 6.0, chains: A,B intermediate substrate analog: N-phosphonomethyl-L-aspartate Apo-structure: 2I3C Resolution: 2,8, R-free: 0,243, pH: - , chains: A,B Ensemble Refinement 2Q51 Resolution: 2,8, R-free: 0,239, pH: - , chains: A,B
For 2O4H, there are only missing residues at the N- and C-terminal ends, which can be neglected:
REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 M RES C SSSEQI REMARK 465 1 ALA A -1 REMARK 465 1 ILE A 0 REMARK 465 1 ALA A 1 REMARK 465 1 THR A 2 REMARK 465 1 SER A 3 REMARK 465 1 CYS A 4 REMARK 465 1 HIS A 5 REMARK 465 1 ILE A 6 REMARK 465 1 ALA A 7 REMARK 465 1 GLU A 8 REMARK 465 1 CYS A 311 REMARK 465 1 LEU A 312 REMARK 465 1 HIS A 313
FoldX
list.txt
2O4H.pdb
individual_list.txt
EA285A; AA305E; GA123E; RA71H; RA71K; KA213E; VA278M; MA82T; EA235K; IA270T;
run.txt
<TITLE>FOLDX_runscript; <JOBSTART>#; <PDBS>#; <BATCH>list.txt; <COMMANDS>FOLDX_commandfile; <BuildModel>#,individual_list.txt; <END>#; <OPTIONS>FOLDX_optionfile; <Temperature>298; <R>#; <pH>7; <IonStrength>0.050; <water>-CRYSTAL; <metal>-CRYSTAL; <VdWDesign>2; <OutPDB>true; <pdb_hydrogens>false; <complex_with_DNA> true; <END>#; <JOBEND>#; <ENDFILE>#;
command
/opt/SS12-Practical/foldx/FoldX.linux64 => choose 3 => run.txt