@TOME V3
(Feb 2022)
Ref.
-
-
Doc.
Global output mode :
Sort entries by :
Atome Result
Tools Result
PDB occurence
3D Alignment Cluster
Sequence Color type :
Secondary Structure
Hydrophobicity
Disulfide Bonds
TCoffee Identity Score
Uniprot annotation
3D Alignment 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
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Structural Clustering:
Cluster Num
3D-Jury Score
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Modeller Result :
Model Rank
QMean Score
Dfire Score
Dope Score
Errat Score
Verify3D Score
Modeller Score
Hide column
Complexes Modeling
PDB Ligands
Affinity Score
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:
Sequence Alignment
Tab of Complexes
Values color: [
Good
|
Correct
|
Middling
|
Bad
]
Modeled complexes 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 model:
[
‹ 3Å
|
‹ 10Å
|
› 10Å
]
Result:
pKd
Quality
PSim.
[
Good
|
Correct
|
Acceptable
| Bad | Empty = ligand not selected during the calculation step or result rejected ]
Query sequence : H_NR1D1_REVa: (2021-05-27 )
MTTLDSNNNTGGVITYIGSSGSSPSRTSPESLYSDNSNGSFQSLTQGCPTYFPPSPTGSLTQDPARSFGSIPPSLSDDGSPSSSSSSSSSSSSFYNGSPPGSLQVAMEDSSRVSPSKSTSNITKLNGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLAEMQSAMNLANNQLSSQCPLETSPTQHPTPGPMGPSPPPAPVPSPLVGFSQFPQQLTPPRSPSPEPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPPATTPHRWENQGCPPAPNDNNTLAAQRHNEALNGLRQAPSSYPPTWPPGPAHHSCHQSNSNGHRLCPTHVYAAPEGKAPANSPRQGNSKNVLLACPMNMYPHGRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLSFRVDAQ
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)
HEM_A_5
(6WMQ)
?
[Raw transfer]
HEM_B_6
(6WMS)
?
[Raw transfer]
COH_A_2
(4N73)
[Raw transfer]
HEM_A_2
(3CQV)
[Raw transfer]
HEM_A_5
(6WMS)
?
[Raw transfer]
HEM_B_6
(6WMQ)
?
[Raw transfer]
22
Blastp_CBE
91.40
71%
-173
- C2 -
6WMS
12.8
?
24
Blastp_CBE
91.27
71%
-178
- C2 -
6WMQ
12.9
?
21
Blastp_CBE
90.95
71%
-177
- C2 -
6WMS
13.0
?
2
PsiBlast_PDB
89.88
71%
-173
- C2 -
4N73
12.5
23
Blastp_CBE
89.67
71%
-166
- C2 -
6WMQ
12.7
?
4
PsiBlast_PDB
87.74
68%
-170
- C2 -
3CQV
12.7
3
PsiBlast_PDB
80.35
73%
-169
- C2 -
2V0V
-
NR1D2_HUMAN
-
17
PsiBlast_PDB
75.06
39%
-192
- C2 -
1S0X
-
-
16
PsiBlast_PDB
73.49
39%
-187
- C2 -
1N83
-
-
15
PsiBlast_PDB
71.62
39%
-183
- C2 -
4S15
-
RORA_HUMAN
-
18
PsiBlast_PDB
70.31
37%
-178
- C2 -
6J1L
-
RORG_HUMAN
-
5
PsiBlast_PDB
70.07
69%
-160
- C2 -
2V7C
-
NR1D2_HUMAN
-
20
PsiBlast_PDB
67.96
37%
-162
- C2 -
5IZ0
-
-
12
PsiBlast_PDB
67.64
40%
-185
* C2 *
1N4H
-
RORB_RAT
-
13
PsiBlast_PDB
66.89
40%
-185
- C2 -
1K4W
-
RORB_RAT
-
14
PsiBlast_PDB
66.80
40%
-187
- C2 -
1NQ7
-
RORB_RAT
-
19
PsiBlast_PDB
65.15
38%
-163
- C2 -
6CN6
-
RORG_HUMAN
-
1
PsiBlast_PDB
44.22
100%
42
- C2 -
3N00
-
NR1D1_HUMAN
-
11
PsiBlast_PDB
28.92
59%
-163
- C1 -
3E00
-
PPARG_HUMAN
-
9
PsiBlast_PDB
27.63
59%
-154
- C1 -
3DZU
-
PPARG_HUMAN
-
