PDBj : : 1

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1 PDB (PDBj) Mar. 3, 2008

2 PDBj : : 1

3 PDBj PDB ID / / XML (xpsss) (Sequence-Navigator) (Structure-Navigator) (ASH) (ProMode) (ef-site) (EM-Navigator) New! GUI (Protein Globe) New! (eprots) (jv) 2

4 PDB PDB format PDB FORTRAN PDBML XML wwpdb XML Schema Westbrook et al. (2005), Bioinformatics 21(7): mmcif ( ) 3

5 PDB : jv3 RasMol PDBML OpenGL Mac, Win, Linux ( Java ) 4

6 5

7 1gof PDB ID 1gof GO 1gof 6

8 : Structural Details 7

9 : Experimental Details (X NMR, ) 8

10 : Functional Details Gene Ontology 9

11 : Sequence neighbor PDB BLAST Sequence Navigator 10

12 : Download / Display PDB PDB PDB mmcif PDB PDB XML PDBML PDBML (no-atom). PDBML (ext-atom) 11

13 : Link PDB RCSB-PDB, MSD-EBI: PDB. CATH, SCOP, FSSP: UniProt: KEGG: EzCatDB: 12

14 Keyword hemoglobin GO 13

15 Advanced Search 14

16 D. M. Standley 15

17 PDB PDB PDBML 16

18 1gof PDB ID 1gof GO 1gof Download/Display 17

19 PDB format 18

20 PDB format all, display PDB format 19

21 PDB format ( ) ( 80 ) 20

22 PDBML XML all, display PDBML ± 21

23 PDBML download <?xml version="1.0" encoding="utf-8"?> <PDBx:datablock datablockname="1gof-noatom" xmlns:pdbx=" xmlns:xsi=" xsi:schemalocation=" pdbx.xsd"> <PDBx:atom_sites_footnoteCategory> <PDBx:atom_sites_footnote id="1"> <PDBx:text>CIS PROLINE - PRO 52</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="2"> <PDBx:text>CIS PROLINE - PRO 163</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="3"> <PDBx:text>CIS PROLINE - PRO 350</PDBx:text> </PDBx:atom_sites_footnote> </PDBx:atom_sites_footnoteCategory> <PDBx:audit_authorCategory> <PDBx:audit_author name="ito, N."></PDBx:audit_author> 22

24 <PDBx:audit_author name="phillips, S.E.V."></PDBx:audit_author> <PDBx:audit_author name="knowles, P.F."></PDBx:audit_author> </PDBx:audit_authorCategory> <PDBx:cellCategory> <PDBx:cell entry_id="1gof"> <PDBx:length_a>98.000</PDBx:length_a> <PDBx:length_b>89.400</PDBx:length_b> <PDBx:length_c>86.700</PDBx:length_c> <PDBx:angle_alpha>90.00</PDBx:angle_alpha> <PDBx:angle_beta>117.80</PDBx:angle_beta> <PDBx:angle_gamma>90.00</PDBx:angle_gamma> <PDBx:Z_PDB>4</PDBx:Z_PDB> </PDBx:cell> </PDBx:cellCategory> <PDBx:database_PDB_matrixCategory> <PDBx:database_PDB_matrix entry_id="1gof"> <PDBx:origx11> </PDBx:origx11>... XML 23

25 : PDB format ATOM 2 CA ALA GOF

26 : PDBML <PDBx:atom_site id="2"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_comp_id>ALA</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_entity_id>1</PDBx:label_entity_id> <PDBx:label_seq_id>1</PDBx:label_seq_id> <PDBx:Cartn_x>38.356</PDBx:Cartn_x> <PDBx:Cartn_y>-0.999</PDBx:Cartn_y> <PDBx:Cartn_z>0.357</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>42.26</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>1</PDBx:auth_seq_id> <PDBx:auth_comp_id>ALA</PDBx:auth_comp_id> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CA</PDBx:auth_atom_id> <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num> </PDBx:atom_site> 25

27 : PDBML (extatom) <PDBx:atom_record id="2"> ATOM 1 A A 1 1?. ALA ALA C CA CA </PDBx:atom_record> 26

28 PDBML Westbrook et al. Bioinformatics (2005) 21(7): XML Schema: 27

29 XML <protein pro_name="a Peptide"> <chain chid="a"> <residue resno="1"> <res_name> ALA </res_name> </residue> <residue resno=" 2"> <res_name> GLY</res_name> </residue> <residue resno=" 3"> <res_name> ILE</res_name> </residue> </chain> </protein> protein pro_name A Peptide chain chid A element name attribute name attribute residue resno 1 residue resno 2 residue resno 3 element ALA GLY ILE XML ( ) (element) (attribute) XML Schema 28

30 XPath XQuery XML PDBj XML XPath XML XQuery XPath 29

31 pdbmlplus XPath/XQuery pdbmlplus citation_authorcategory citationcategory citation journal_abbrev journal_volume page_first datablock datablock = PDB ID (J. Biol. Chem. ) Volume 30

32 entity_src_natcategory entity_src_nat common_name pdbx_organism_scientific exptlcategory exptl method... (Human) (Homo sapiens) (NMR, X-ray, etc.) 31

33 xml-based Protein Structure Search Service (xpsss) xpsss XQuery XPath 32

34 XPath /datablock[ ] / 33

35 XPath (1) PDB ID 34

36 XPath (2) datablock citation_authorcategory 35

37 XPath (3) (1gof) 1GOF-noatom ] /citation_authorcategory/citation_author/@name Ito, N. /datablock[ citation_authorcategory/citation_author/@name= Ito, N. ] /@datablockname 36

38 XPath (4) /datablock[entitycategory/entity/formula_weight >= 30 /datablock[struct_confcategory/struct_conf/pdbx_pdb_helix_length >= 30] /datablock[ entitycategory/entity/formula_weight >= and struct_confcategory/struct_conf/pdbx_pdb_helix_length >= 30] 37

39 XQuery for... where... return where for $b in input()xpath where $b return <datablock> { 1} { 2} { 3}... </datablock> 38

40 XQuad: XQuery Advisor for PDBML 1. XQuery XQuery XQuad 39

41 XQuad xpsss XQuad XQuad 40

42 XQuery 1) Category / Keyword 2) Select Tags or Check XQuery 3) Fill in Condition 4) Submit! 41

43 42

44 (eprots) 43

45 Protein Globe: PDBj GUI 44

46 jv3 PDBj jv3 (PDBjViewer version 3) 1. Java (JRE ) 2. jv version3 3. ( JOGL JSR Web jv3 4. jv binary ( ) jv 5. 45

PDB データの読み解き方 mmcif と PDBML 金城玲大阪大学蛋白質研究所 PDBj講習会 1

PDB データの読み解き方 mmcif と PDBML 金城玲大阪大学蛋白質研究所この講義の内容 PDB の新しいフォーマットの必要性 PDB の新しいフォーマットである mmcif その XML への直訳である PDBML mmcif と PDBML の基礎である PDBx 辞書これらの具体例 2 PDB の新フォーマット旧フォーマットはいわゆる PDB ファイルのフォーマットのこと