@TOME V2.2
(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 : T0801: (2014-06-02 )
MIPFNAPPVVGTELDYMQSAMGSGKLCGDGGFTRRCQQWLEQRFGSAKVLLTPSCTASLEMAALLLDIQPGDEVIMPSYTFVSTANAFVLRGAKIVFVDVRPDTMNIDETLIEAAITDKTRVIVPVHYAGVACEMDTIMALAKKHNLFVVEDAAQGVMSTYKGRALGTIGHIGCFSFHETKNYTAGGEGGATLINDKALIERAEIIREKGTNRSQFFRGQVDKYTWRDIGSSYLMSDLQAAYLWAQLEAADRINQQRLALWQNYYDALAPLAKAGRIELPSIPDGCVQNAHMFYIKLRDIDDRSALINFLKEAEIMAVFHYIPLHGCPAGEHFGEFHGEDRYTTKESERLLRLPLFYNLSPVNQRTVIATLLNYFS
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)
PMP_A_2
(1MDO)
ARNB_SALTY
[Raw transfer]
PLP_A_3
(1MDZ)
ARNB_SALTY
[Raw transfer]
PMP_A_3
(2C81)
GLDSA_BACCI
[Raw transfer]
PLP_A_2
(1MDX)
ARNB_SALTY
[Raw transfer]
CIT_A_3
(4LC3)
?
[Raw transfer]
AKG_A_3
(1MDX)
ARNB_SALTY
[Raw transfer]
35
HHSearch
91.48
31%
-107
- C1 -
3DR4
-
?
-
5
PsiBlast_PDB
91.45
33%
-103
- C1 -
1MDO
4.5
ARNB_SALTY
1
PsiBlast_PDB
90.76
33%
-104
- C1 -
1MDX
3.2
ARNB_SALTY
36
HHSearch
90.09
31%
-103
- C1 -
4LC3
-
?
-
34
HHSearch
89.81
32%
-100
* C1 *
1MDO
-
ARNB_SALTY
-
42
HHSearch
88.98
30%
-110
- C1 -
2OGA
-
?
-
43
HHSearch
87.19
30%
-118
- C1 -
4K2M
-
NTDA_BACSU
-
2
PsiBlast_PDB
87.04
33%
-102
- C1 -
1MDZ
3.0
ARNB_SALTY
6
PsiBlast_PDB
86.50
31%
-101
- C1 -
4LC3
2.7
?
32
HHSearch
86.35
31%
-101
- C1 -
3BB8
-
?
-
28
HHSearch
84.38
29%
-103
- C1 -
2C81
4.2
GLDSA_BACCI
41
HHSearch
84.23
26%
-106
- C1 -
2PO3
-
?
-
12
Fugue
84.10
28%
-115
- C1 -
4K2M
-
NTDA_BACSU
-
37
HHSearch
83.33
30%
-104
- C1 -
3NYT
-
WBPE_PSEAE
-
31
HHSearch
83.29
30%
-108
- C1 -
3FRK
-
?
-
39
HHSearch
82.64
26%
-112
- C1 -
3UWC
-
?
-
8
Fugue
82.58
25%
-111
- C1 -
1O69
-
?
-
38
HHSearch
82.01
24%
-111
- C1 -
2FNU
-
PSEC_HELPY
-
3
PsiBlast_PDB
81.84
31%
-107
- C1 -
3DR4
-
?
-
33
HHSearch
79.03
24%
-109
- C1 -
1O69
-
?
-
User Run . : Multi Template Modeling Result:
(5 SA)
Binding Score for complex ligand / Scwrl (Unconserved SChains Recalculated) model
(Only selected ligand are displayed)
(Atome)
(Ident)
(Tito)
(Num)
(pKd)
(Uniprot)
PMP_A_2
(1MDO)
ARNB_SALTY
[Raw transfer]
PLP_A_3
(1MDZ)
ARNB_SALTY
[Raw transfer]
PMP_A_3
(2C81)
GLDSA_BACCI
[Raw transfer]
PLP_A_2
(1MDX)
ARNB_SALTY
[Raw transfer]
CIT_A_3
(4LC3)
?
[Raw transfer]
AKG_A_3
(1MDX)
ARNB_SALTY
[Raw transfer]
57
99.96
100%
-122
- C- -
M057
-
-
58
99.62
100%
-127
- C- -
M058
-
-
61
99.11
100%
-130
- C- -
M061
-
-
63
97.22
100%
-120
- C- -
M063
-
-
51
29.06
100%
-37
- C- -
M051
-
-
