IDInstanceStatusSelectionDetailsScore LIGA505 LIGAND CODE MATCHED XYZ XYPA503CLOSE MATCH XYPA504NO...
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Transcript of IDInstanceStatusSelectionDetailsScore LIGA505 LIGAND CODE MATCHED XYZ XYPA503CLOSE MATCH XYPA504NO...
ID Instance Status Selection Details Score
LIG A505 LIGAND CODE MATCHED XYZ
XYP A503 CLOSE MATCH
XYP A504 NO MATCH
MAN A500 PASSED
GLC A501 PASSED
NAG A502 PASSED
2010/09/01 JY1
Batch Search SummaryQuery type: Default
Show Details
Instance Search
Save
Rerun BatchInput new parameters here
When you change parameters, those will be displayed here
Input your notes here
Show Details
Show Details
Show Details
Show Details
Show Details
New window will pop-up with log file;Details are to be discussed.
Ligand Module:Level 1- Batch Search Report (pre-searched)
Help
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.
Capture processing details in proc cycle
Finish
Save and come back later
Save and complete ligand module
Rerun Batch Create new ligand
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?
XX
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)
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Level 2- Instance Search UI
Run Global
Split/Merge
Group all the ligands that have the same 3 letter
Force Match
ID Score (%)
Selection for comparison
0AI 98
1NA 97
5AX 96
A2G 96
Model CC
Input new parameters here
Input your notes here
COMPARE
Show Hydrogens
Show Lables
Create new ligand
Select Extracted Ligands: XYP LIG
XYP_B_287 ID Instance StatusSelection for force
match, edit or create new
XYP A503 CLOSE MATCH
XYP A504 NO MATCH
More XYP ligands to be displayed on this page with scroll bar
Selected Ligand instances Selected Ligand instances
Search results for Ligand instances Search results for Ligand instances
XYP_B_287
Note: Using the above table, you can select more than one instances for force match.
Run Instance search
Note: Have drop down options for table or sketch
Save Undo
Ligand Module:Level 2 – Instance Search UI --> Drilldown to Detailed Report I
COMPARE
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Search Result SummaryResult 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
Target formula: C8 H15 N O5
Authors Name: 1,5-anhydro-2-(acetylamino)-2-deoxy-D-glucitol
Authors Formula: C8 H15 N O5
ID Formula Name Score (%)
Selection for compariaon
0AI C9 H15 N O7 methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranosiduronic acid 98
1NA C9 H17 N O6 N-ACETYL-O-METHYL-D-GLUCOSAMINE 97
5AX C8 H15 N O5 2-(ACETYLAMINO)-1,5-ANHYDRO-2-DEOXY-D-GLUCITOL 96
A2G C8 H15 N O6 N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE 96
BGN C10 H19 N O6 N-BUTANOYL-2-AMINO-2-DEOXY-GLUCOPYRANOSIDE 95
dictionary link to subject link to comparative
report
Scoring algorithm to be discussed
SEE ALL
Force Match
XYP_B_287
Save Undo
Ligand Module:Level 2 – Instance Search UI --> Drilldown to Detailed Report II: Comparative output
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Interactive atom-level mapping including stereo-chemistry.Clicking on the atom in the table will highlight the atom in the 3D graph and vice versa (on all instances).
2D and 3D side-by-side comparison
Author Query Subject(deposited info) (model coordinates) (ideal coordinates)
FORCE MATCH CREATE NEW LIGAND
APC C5 N ABG C6 NAPC C4 R ABG C5 RAPC O4 N ABG O3 NAPC C3 S ABG C4 SAPC O3 N ABG O4 NAPC C2 R ABG C2 RAPC O2 N ABG O2 NAPC C1 S ABG C1 R
3/22 MZ GS CS
Formula: C11 H19 N1 O9
Name: Adenosyl …Formula: C11 H19 N1 O9
Name: Diphospho…
Author’s 2D & 3D viewAuthor’s 2D & 3D view
Save Undo
Ligand Module:Level 3 – Edit UI – Structure Edit
Model CCView report or Chemical mmCIF file
View report
View CC file
Add to CVS
Note: automatically validate and check for duplicated ligands before adding to CVS
Save UndoModify exist ligand
Input ligand 3 letter code
Reconcile and check for duplicate ligands, the newly created ligand must be available for
search immediately
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?
Version Date Annotator SIte Modify type Modify details
1 1997-03-01 CS RCSB Linking type
2 2003-04-01 MZ RCSB parent
Ligand Module:Level 3 – Edit UI – Text Edit (collapsed)
Model CCView report or Chemical mmCIF file
View report
View CC file
Add to CVS
Note: automatically validate and check for duplicated ligands before adding to CVS
Save Undo
Input ligand 3 letter code Note: model database code should be automatically generated
Note: Type and NDB type should be updated automatically if parent info is provided
Version Date Annotator SIte Modify type Modify details
1 1997-03-01 CS RCSB Linking type
2 2003-04-01 MZ RCSB parent
Modify exist ligand
Ligand Module:Level 3 – Edit UI – Text Edit (expanded)
Model CCView report or Chemical mmCIF file
View report
View CC file
Add to CVS
Note: automatically validate and check for duplicated ligands before adding to CVS
Save UndoInput ligand 3 letter code
Note: when save button clicked, check parent and linking type,
then automatically update atom names again
Allow add/delete rows
Mouse over function[SIA]1:A.C2 #9 1.65 0.229 -3.721
Add 2D and 3D view with mouse over functions
Version Date Annotator SIte Modify type Modify details1 1997-03-01 CS RCSB Linking type
2 2003-04-01 MZ RCSB parent
ID NAGName N-ACETYL-D-GLUCOSAMINE Type D-SACCHARIDE
PDBx type ATOMS Formula C8 H15 N O6Parent
SynonymsFormal charge
Ambiguous flagCreation dateID replaced by
ID replacesOne letter code
Subcomponent list
Atom name Element type Charge Aromatic flag Leaving atom flag chiral center flag Subcomponent residue name Linking atom flag
C1 C 0 Pull down Y/N Pull down Y/N Pull down R,S,N Pull down N-terminal, C-terminal, central
C2 C 0 Pull down Y/N Pull down Y/N Pull down R,S,N Pull down N-terminal, C-terminal, central
C3 C 0 Pull down Y/N Pull down Y/N Pull down R,S,N Pull down N-terminal, C-terminal, central
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
Modify exist ligand
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 codeLigand match XXX: Exact match for all atom types, number of atoms and connectivity except the 3 letter codeClose match: exact match for all atom types and connectivity, but not the number of atoms (query could have less atoms) nor the chiralityNo 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 nomenclatureModified nucleic acids should follow standard nucleic acid nomenclatureAll sugars should follow standard sugars nomenclatureOthers 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 N-terminal, 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.