Transcript Ligand Module

Ligand Module:
Level 1- Batch Search Report (pre-searched)
Batch Search Summary
Query type:
ID
When you change parameters,
those will be displayed here
Default
Instance
Status
LIG
A505
LIGAND CODE
MATCHED XYZ
Show Details
XYP
A503
CLOSE MATCH
Show Details
XYP
A504
NO MATCH
Show Details
MAN
A500
PASSED
Show Details
GLC
A501
PASSED
Show Details
NAG
A502
PASSED
Show Details
Instance Search
Rerun Batch
Selection
Details
1
Create Rerun
new ligand
Batch
Save
Save and come
back later
X
Finish
Save and complete
ligand module
Score
Input new parameters here
Input your notes here
Help
Upon closing window browser from the top
right corner, tool should pop up a window and
provide 3 options before closing window:
Save? Cancel? No save?
Capture processing details in proc cycle
Batch Search: Automatically search all ligand instances in an entry
against CCD/PRD and report the results before annotators begin
annotation.
Instance search: Annotators review and select instances that are
failed from batch search (not passed) and perform search with
different parameters or force to pass (force match)
New window will pop-up with log file;
Details are to be discussed.
Table is sorted by status (order: no match, close
match, ligand code matched XXX, passed), then by 3
letter code
Passed: Exact match for all atom types,
number of atoms, connectivity and 3 letter
code
Ligand match XXX:
Exact match for all atom types, number of
atoms and connectivity except the 3 letter
code
Close match: exact match for all atom types
and connectivity, but not the number of
atoms (query could have less atoms) nor the
chirality
No match: none of above, treat as a new
ligand.
2010/09/01 JY
Level 2- Instance Search UI
Select Extracted Ligands:
XYP
Group all the ligands
that have the same 3
letter
Undo
LIG
Selected Ligand instances
Run Global
XYP_B_287
Model CC
Split/Merge
ID
Instance
Status
XYP
A503
CLOSE
MATCH
XYP
A504
NO MATCH
Run Instance search
Search results for
Ligand instances
Input new parameters here
Input your notes here
Show Hydrogens
XYP_B
_287
ID
Show Lables
0AI
1NA
5AX
A2G
2
Selection for force
match, edit or create
new
Note: Using the above table, you can select
more than one instances for force match.
Note: Have drop down options for table or
sketch
Create new ligand
Save
More XYP ligands to be displayed on this
page with scroll bar
Force Match
Score Selection for
(%)
comparison
98
97
96
96
COMPARE
Ligand Module:
Level 2 – Instance Search UI --> Drilldown to Detailed Report I
Undo
Search Result Summary
Result count: 23 , top 5 shown
Query file:
NAG L 741
Query type:
Close (formula bounded)
Target name: 2-(acetylamino)-1,5-anhydro-2-deoxy-D-glucitol
Scoring algorithm to
be discussed
Target formula: C8 H15 N O5
Authors Name: 1,5-anhydro-2-(acetylamino)-2-deoxy-D-glucitol
Authors Formula: C8 H15 N O5
XYP_B
_287
ID
Name
0AI
C9 H15 N O7
methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranosiduronic
acid
1NA
C9 H17 N O6
N-ACETYL-O-METHYL-D-GLUCOSAMINE
5AX
C8 H15 N O5
2-(ACETYLAMINO)-1,5-ANHYDRO-2-DEOXY-D-GLUCITOL
A2G
C8 H15 N O6
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
BGN
C10 H19 N O6
N-BUTANOYL-2-AMINO-2-DEOXY-GLUCOPYRANOSIDE
Force Match
3
Formula
SEE ALL
dictionary link
to subject
Score
(%)
Selection for
compariaon
98
97
96
96
95
COMPARE
link to comparative
report
Save
Undo
Ligand Module:
Level 2 – Instance Search UI --> Drilldown to Detailed Report II: Comparative output
Author
(deposited info)
Query
Subject
(model coordinates)
(ideal coordinates)
Formula: C11 H19 N1 O9
Name: Adenosyl …
Save
Formula: C11 H19 N1 O9
Name: Diphospho…
Author’s 2D & 3D view
2D and 3D sideAPC
by-side
APC
APC
comparison
APC
APC
APC
APC
APC
4
C5
C4
O4
C3
O3
C2
O2
C1
N
R
N
S
N
R
N
S
FORCE MATCH
ABG
ABG
ABG
ABG
ABG
ABG
ABG
ABG
CREATE NEW LIGAND
C6
C5
O3
C4
O4
C2
O2
C1
N
R
N
S
N
R
N
R
Interactive atom-level
mapping including stereochemistry.
Clicking on the atom in the
table will highlight the
atom in the 3D graph and
vice versa (on all
instances).
3/22 MZ GS CS
Ligand Module:
Level 3 – Edit UI – Structure Edit
Version
Date
Annotator
1
1997-03-01 CS
2
2003-04-01 MZ
Undo
Input ligand 3 letter code
Modify exist ligand
SIte
Modify type
RCSB
RCSB
Linking type
Save
Modify details
parent
The tool should check for 3 letter code. If the
code is unique to the dictionary, it will retain
the 3 letter code. If the code already exists in
the dictionary, the tool will automatically
assign a unique 3 letter code. Should there be
a hard coded black list for bad ligand codes?
Reconcile and check for duplicate ligands, the
newly created ligand must be available for
search immediately
View report
orCC Chemical
Model
mmCIF file
View
report
View
CC file
Add to
CVS
Note: automatically validate and check for
duplicated ligands before adding to CVS
Ligand Module:
Level 3 – Edit UI – Text Edit (collapsed)
Undo
Modify exist ligand
Version
Date
Annotator
1
1997-03-01 CS
2
2003-04-01 MZ
Input ligand 3 letter code
SIte
Modify type
RCSB
RCSB
Linking type
Save
Note: model database code should be
automatically generated
Modify details
parent
Note: Type and NDB type should be updated
automatically if parent info is provided
View report
orCC Chemical
Model
mmCIF file
View
report
View
CC file
Add to
CVS
Note: automatically validate and check for
duplicated ligands before adding to CVS
Ligand Module:
Level 3 – Edit UI – Text Edit (expanded)
Modify exist ligand
Version
Date
Annotator
1
1997-03-01 CS
SIte
RCSB
Modify type
Linking type
2
RCSB
parent
2003-04-01 MZ
ID
Name
NAG
N-ACETYL-D-GLUCOSAMINE
Type
D-SACCHARIDE
PDBx type
ATOMS
Formula
C8 H15 N O6
Input ligand 3 letter code
Undo
Save
Modify details
Note: when save button clicked,
check parent and linking type,
then automatically update atom
names again
Add 2D and 3D view
with mouse over
functions
Mouse over function
Parent
Synonyms
Formal charge
Ambiguous flag
Creation date
ID replaced by
ID replaces
[SIA]1:A.C2 #9 1.65 0.229 -3.721
One letter code
Subcomponent list
Atom name Element type
Charge
Aromatic flag
Leaving atom flag
C1
C
0
Pull down Y/N
Pull down Y/N
C2
C
0
Pull down Y/N
Pull down Y/N
C3
C
0
Pull down Y/N
Pull down Y/N
Atom 1
Atom 2
Bond order
Aromatic flag
C1
C2
Pull down
SING/DOUB
Pull down Y/N
C1
O1
Pull down
SING/DOUB
Pull down Y/N
C2
C3
Pull down
SING/DOUB
Pull down Y/N
View report
orCC Chemical
Model
mmCIF file
View
report
chiral center flag
Subcomponent residue name
Linking atom flag
Pull down R,S,N
Pull down N-terminal,
C-terminal, central
Pull down R,S,N
Pull down N-terminal,
C-terminal, central
Pull down N-terminal,
C-terminal, central
Pull down R,S,N
View
CC file
Add to
CVS
Allow add/delete
rows
Note: automatically validate and check for
duplicated ligands before adding to CVS
1. At deposition- validate atom name against element type to resolve the shifted column
issue, for example chlorine vs carbon, carbon vs calcium
2. Instance search UI will provide command line for parameter change, no graph edit tool
required.
3. Close match is defined as exact match for all atom types and connectivity, but not the
number of atoms (query could have less atoms) nor the chirality. Chirality is relaxed so that it
can find all the possible stereochemistry and rank the order (scoring) by the best match of
stereochemistry.
Definition of status is defined as below:
Passed: Exact match for all atom types, number of atoms, connectivity and 3 letter code
Ligand match XXX:
Exact match for all atom types, number of atoms and connectivity except the 3 letter code
Close match: exact match for all atom types and connectivity, but not the number of atoms
(query could have less atoms) nor the chirality
No match: none of above, treat as a new ligand.
4. Score: it should be based on the # of missing atoms and # of matched chiral centers.
Annotators suggest software team to consult with Kim/Terry on this. In the mean time Guarav
will look for someone to consult with CCDC.
5. Atom nomenclature: Jasmine discussed w/ Jawahar after Kim’s visit at RCSB that
the atom nomenclature should be standardized as below when creating new ligands:
Modified amino acids should follow standard amino acid nomenclature
Modified nucleic acids should follow standard nucleic acid nomenclature
All sugars should follow standard sugars nomenclature
Others should begin with atom type followed by number, for example, C1, C2, CL1, etc
instead of CAA, CAB, CLA, etc.
The system can recognize the first 3 by looking for parent residue or linking type
(whether it is peptide linking or nucleotide linking or saccharide linking).
6. Relax chiral center for close match: It is recommended to search based on 3 letter
code first, if no match found, then look for possible stereo isomers. This is based on
the work practice that most of the sugars have wrong chirality in the coordinates. If 3
letter code match, however one or more of the chiral centers is (are) flat, it should
report as close match and state the discrepancy, for example, planar found at C1
center.
7. Please note that request of new cif tokens are added to the CCD to identify Nterminal, or C-terminal or central heavy atom. This is for calculate the distance on
neighboring residues when there is a break in the coordinates where C or N atoms
may not be observed.