Batch Search Summary Query type: Default

1. Ligand Module: Level 1- Batch Search Report (pre-searched) X 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? Batch Search Summary Query type: Default When you change parameters, those will be displayed here Finish Save Save and come back later Save and complete ligand module 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. Input new parameters here Input your notes here Rerun Batch 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) Rerun Batch Create new ligand Instance Search Help Show Details Show Details Show Details Show Details Show Details Show Details 2010/09/01 JY

2. Level 2- Instance Search UI Group all the ligands that have the same 3 letter XYP Select Extracted Ligands: LIG Selected Ligand instances Save Undo Run Global XYP_B_287 Model CC Note: Using the above table, you can select more than one instances for force match. Note: Have drop down options for table or sketch Input new parameters here Search results for Ligand instances Input your notes here XYP_B_287 Show Hydrogens Show Lables Create new ligand Force Match Split/Merge COMPARE Run Instance search More XYP ligands to be displayed on this page with scroll bar

3. Ligand Module:Level 2 – Instance Search UI --> Drilldown to Detailed Report I 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 Target formula: C8 H15 N O5 Authors Name: 1,5-anhydro-2-(acetylamino)-2-deoxy-D-glucitol Authors Formula: C8 H15 N O5 Save Undo Scoring algorithm to be discussed XYP_B_287 dictionary link to subject Force Match COMPARE SEE ALL link to comparative report

4. Ligand Module:Level 2 – Instance Search UI --> Drilldown to Detailed Report II: Comparative output Author Query Subject (deposited info) (model coordinates) (ideal coordinates) Save Undo Formula: C11 H19 N1 O9 Name: Adenosyl … Formula: C11 H19 N1 O9 Name: Diphospho… Author’s 2D & 3D view 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 APC C5 N ABG C6 N APC C4 R ABG C5 R APC O4 N ABG O3 N APC C3 S ABG C4 S APC O3 N ABG O4 N APC C2 R ABG C2 R APC O2 N ABG O2 N APC C1 S ABG C1 R CREATE NEW LIGAND 3/22 MZ GS CS FORCE MATCH

5. Ligand Module:Level 3 – Edit UI – Structure Edit Input ligand 3 letter code Save Undo 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 Add to CVS View CC file Modify exist ligand View report or Chemical mmCIF file Note: automatically validate and check for duplicated ligands before adding to CVS Model CC

6. Ligand Module:Level 3 – Edit UI – Text Edit (collapsed) Note: model database code should be automatically generated Input ligand 3 letter code Save Undo Note: Type and NDB type should be updated automatically if parent info is provided View report Add to CVS View CC file Modify exist ligand View report or Chemical mmCIF file Note: automatically validate and check for duplicated ligands before adding to CVS Model CC

7. Ligand Module:Level 3 – Edit UI – Text Edit (expanded) Input ligand 3 letter code Save Undo 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 [SIA]1:A.C2 #9 1.65 0.229 -3.721 Allow add/delete rows View report Add to CVS View CC file Modify exist ligand View report or Chemical mmCIF file Note: automatically validate and check for duplicated ligands before adding to CVS Model CC

8. 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.

9. 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 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.