@TOME V2.3
(Nov 2016)
Ref.
-
-
Doc.
Global output mode :
Sort entries by :
Atome Result
Tools Result
PDB occurence
Core Structure Cluster
Sequence Color type :
Secondary Structure
Hydrophobicity
Disulfide Bonds
TCoffee Identity Score
Uniprot annotation
Core Structure Cluster
Contacts with Ligands
Show alignment :
Atome selection
All alignments
Only Template with Ligand
Column output:
Score:
Atome Rank Value
Tools Score
Hide column
Alignment:
Sequence Identity (%)
Tcoffee Alignment Score
Hide column
3D Common Core:
Tito PKB Score
Verify3D Score
QMean Score
Hide column
Structural Clustering:
Cluster Num
3D-Jury Struct. Score
Hide column
Modeller Result :
Model Rank
QMean Score
Dfire Score
Dope Score
Errat Score
Verify3D Score
Modeller Score
Hide column
Complexes Modeling
Show Ligands of Templates
Complexes Affinity Score
Main Binding Site Identity
Hide column
Templates Information:
Uniprot entry
Cath class
Scop class
Smart class
Prosite class
Pfam class
EC Number
Taxonomy
Experiment Method
Hide column
Sequence & Result Tab:
PDB Template Sequence
Complexes Tab
Values color: [
Good
|
Correct
|
Middling
|
Bad
]
Comparative Docking Tab:
Displays
the 10 best
the 20 best
All
ligands Score after transfer from template to
Tito
Scwrl (Raw)
Scwrl (All SChains of Binding Site Recalculated)
Scwrl (Unconserved SChains of Binding Site Recalculated)
Modeller
model
Cell color: RMS between binding site of experimental template and receptor:
[
‹ 3Å
|
‹ 10Å
|
› 10Å
]
Result:
pKd
Quality
PSim.
[
Good
|
Correct
|
Acceptable
| Bad | Empty = ligand not selected during the calculation step or result rejected ]
Query sequence : PA4234: (2016-02-25 )
MDKILIRGARTHNLKNVDLTLPRDKLIVITGLSGSGKSSLAFDTLYAEGQRRYVESLSAYARQFLSMMEKPDVDTIEGLSPAISIEQKSTSHNPRSTVGTITEIYDYLRLLYARVGTPRCPDHDIPLEAQTVSQMVDQVLALPEGSKLMLLAPVIRERKGEHLAVFDEMRAQGFVRARVDGKLYELDEVPKLDKQKKHSIDVVVDRFKVRADLQQRLAESFETALSLADGIALVAPMDEDEDVEEIIFSARFACPVCGHSISELEPKLFSFNNPAGACPTCDGLGVKQFFDARRVVNGELTLAEGAIRGWDRRNVYYFQMLGSLAQHYGFSLEEPFDELGAEHQKVVLYGSGRENVDFRYLNDRGDIVKRSHPFEGILPNLERRYRETESATVREELAKFLSTQPCPDCHGTRLRREARHVWVGDRTLPAITAMPVGEACEYAAGLSLTGRRGEIAAKILKEIRDRLQFLVNVGLDYLTLDRSADTLSGGEAQRIRLASQIGAGLVGVMYILDEPSIGLHQRDNERLLGTLTHLRNLGNTVIVVEHDEDAIRLADYVVDIGPGAGVHGGQVVAEGTPDQVMNHPDSLTGKYLSGRKKIAVPAKRTPRDKKKLLKLKGARGNNLQNVNLEIPVGLFTCITGVSGSGKSTLINNTLFPITATALNGATTLEVAPYDSFDGLQHLDKVVDIDQSPIGRTPRSNPATYTGLFTPIRELFSGVPEARSRGYGPGRFSFNVKGGRCEACQGDGVIKVEMHFLPDIYVPCDVCKGKRYNRETLEIRYKGKSIHEVLEMTIEEAREFFDAVPALARKLQTLMDVGLSYIKLGQSATTLSGGEAQRVKLSRELSKRDTGKTLYILDEPTTGLHFADIQQLLDVLHRLRDHGNTVVVIEHNLDVIKTADWLVDLGPEGGSKGGQIIANGTPEQVAEMPQSHTGHFLKPLLERDRA
Atome Classification :
(20 SA)
Binding Score for complex ligand / Scwrl (Unconserved SChains Recalculated) model
(Only selected ligand are displayed)
(Atome)
(Ident)
(Tito)
(Num)
(pKd)
(Uniprot)
PPV_A_4
(3PIH)
UVRA_THEMA
[Raw transfer]
1
PsiBlast_PDB
95.95
62%
-94
- C2 -
3UWX
-
?
-
2
PsiBlast_PDB
92.23
61%
-94
- C2 -
2R6F
-
?
-
114
HHSearch
91.88
62%
-94
- C2 -
2R6F
-
?
-
3
PsiBlast_PDB
90.93
57%
-83
- C2 -
3ZQJ
-
UVRA_MYCTU
-
23
PsiBlast_CBE
87.79
57%
-82
- C2 -
3ZQJ
-
UVRA_MYCTU
-
21
PsiBlast_CBE
87.09
57%
-82
- C2 -
3ZQJ
-
UVRA_MYCTU
-
22
PsiBlast_CBE
86.71
57%
-82
- C2 -
3ZQJ
-
UVRA_MYCTU
-
113
HHSearch
75.42
43%
-76
* C2 *
2VF7
-
?
-
4
PsiBlast_PDB
66.03
41%
-67
- C2 -
2VF7
-
?
-
5
PsiBlast_PDB
65.93
41%
-67
- C2 -
2VF8
-
?
-
26
PsiBlast_CBE
65.90
41%
-67
- C2 -
2VF7
-
?
-
25
PsiBlast_CBE
65.74
41%
-67
- C2 -
2VF7
-
?
-
24
PsiBlast_CBE
65.47
41%
-65
- C2 -
2VF8
-
?
-
116
HHSearch
57.84
39%
-79
- C2 -
3PIH
3.2
UVRA_THEMA
120
HHSearch
55.93
38%
-70
- C2 -
2R6F
-
?
-
117
HHSearch
55.36
35%
-69
- C2 -
2VF7
-
?
-
121
HHSearch
47.29
25%
-53
- C2 -
1YQT
-
?
-
118
HHSearch
47.23
26%
-52
- C2 -
3BK7
-
?
-
137
Fugue
46.03
62%
-79
* C5 *
4DFC
-
UVRA_ECOLI
-
6
PsiBlast_PDB
45.91
62%
-79
- C5 -
4DFC
-
UVRA_ECOLI
-