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Search by PDB Entry and Molecule Annotation

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Step-by-step guide of ligand annotation validation with ValidatorDB (http://ncbr.muni.cz/ValidatorDB). Validation results for molecules with specific annotations, from selected PDB entries.

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Search by PDB Entry and Molecule Annotation

  1. 1. VCJIICIOIOTDB Step-by-step guide
  2. 2. I. I'm looking for the validation results for molecules with specific annotation in selected PDB entries
  3. 3. ,. First T me Wiki Manua Database of validation results for ligands and non-standard residues in the Protein Data Bank. Database last updated 16I10I2014: 104126 enlies from PDB. org, 2A3597 molemles relevant for validaion, 17991 models from wwPDB CCD. The moiewies deemed relevant tor valdatiori are al hgands and non-standard residues wnh reasonable size [more than six heavy atoms) Standard ammo acids and nucleotides are not covered The vaidation is performed agaiist models from wwPDE Chemical Component Dictionary iwwPDB CCD) The database is updated weekly Quick Help Samples Overview Details by Molecule Details by PDB Entry This is the Validatorm’ synopsis page. Access different tabs for overviews and statistical evaluation of the validation results. in graphical or tabular form. specific results can be examined in deeper detail by accessing the Validatorm’ specifics page. Different sections of the web page offer interactive guides indicated by E which give a quick walk through all the main elements of the page. Further help is provided by the info icons 0. Many tool tips are available by hovering over any graphical or textual element in the Interface. Refer to the Wiki for any clarifications (especially Terminology and User Interface). Firs! Tlmt Usitr? Check out the First Time User Hesentetion. X @2014 David Sehnal Click the Search tab. ..
  4. 4. - DB 9 Guide First Time User VWKI Manual Database of validation results for ligands and non-standard residues in the Protein Data Bank. Database last updated 16I10I2014: 104126 entriesfiom PDB org. 243597 molecules relevantforvalidation. 17937 models from wwPDB CCD The nioieciiies deemed ielevaritioi validation are all ligands and non-standard residues with reasonable si: e imore than SIX heavy atomsi Standard amino acids and nucleotides are not covered The uialidatioii I5 pervorrned against models from 'l'lPDB Chemical Component oictionm l'n‘IPDB ccoi The database IS updated 'leekt'/ Quick Help Samples Search Overview Details by Molecule Details by PDB Entry PDB Entry and Molecule Annotation vandauon resuls ior molecules with specific annotations. rrom sebcted PDB enines Search by PDB Entry MOIIEUII Idilllifiif MOIOEIJII Annotation Cc) 2014 David Sehnal Select the criterion Search by PDB Entry and Molecule Annotation.
  5. 5. Ulde FIFSI Time User VWKI Manual Validator°B Database of validation results for ligands and non-standard residues in the Protein Data Bank. Database last updated 16I10I2014: 104126 entries lrom PDB org. 243597 molecules relevantforvalioation. 17937 models from wwPDB CCD The molecules deemed relevant tor validation are all ligands and non-standard residues with reasonable si: e imore than six heavy atomsi Standard amino ZDGS and nucleotides are not covered The validation is penomied against models from WWPDB Chemical Component Dictionary IWWPDB ccni The database is updated weekly Quick Help Samples Search Overview Details by Molecule Details by PDB Entry Search by PDB Entry Moloculc Identifier Moloculo Annotation PDB Entry and Molecule Annotation Search by PDB Entry and Molecule Annotation Validation results for molecules with Sp8C| ‘lC annotations from selected PDB entries PDB Entries eg 3Dt2 A list olPDB entry identifiers, separated by a newline or a comma. 0 Molecule Annotations A Iistofmoiecuies identified by their residue 3»| etter codes, separated by a newline ora comma. ~ Enter some PDB identifiers In New Tab Reques1 up to 10 terns to get Instantaneous results iouiix Searotll Larger searches might take several mllules to complete lsiow Search]. Fill in the list of PDB Entry IDs and molecule annotations you are interested in. Sepgggtedtshhern either with a comma or Cl newline.
  6. 6. Uide First Time US6f VVIKI Manual Validator°B Database of validation results for ligands and non-standard residues in the Protein Data Bank. Database last updated 16I10I2014: 104126 entries from PDB org. 243591 molecules relevanlforvalidation. 17997 models from wwPDB (:00 The nioleciiles deemed ielevanlioi validation aie all iigaiias and Mm-S1arI0ald iesidiies i-mri ieasoiiable sl: e imoie than Si» rieaw aloiiisi Standard amino ams and nucleotides aie not covered The validation is perromied against models flolll i-/ i-inns Chenlllzal Component Dictionary‘ ii-MPDB com The aaianase IS updated Weekly‘ Quick Help Samples Search Overview Details by Molecule Details by PDB Entry Search by PDB Entry Molecule Identifier Molecule Annotation PDB Entry and Molecule Annotati Search by PDB Entry and Molecule Annotation| 0Examp| e1 -d i L: E CTTHC“3 2'diiijr]UUH ii: -suits *i: ii r*‘icilci: ulr: -5 : .i: ri Sp: -i: i'ii: arnonticins ‘lam SC PDB Entries 1 entclbri 3012 / e A list of PDB entry identifiers, separated by a newline or a comma 0 Molecule Annotations 1 emeiea NAG A A list ofmolecules identified by their residue 3-letter codes. separated by a newline ora comma O N equ up o I ems oge In an aneousresus u. argersear mig aesevera mnues ocom e v ar For start see the Example 1. Click on it and press Search. iazwoaviasennan
  7. 7. §JSON °-e-. i -3-. 'i'i’i: r‘I. ',iciiiir. Search — 3D12 l NAG Overview Details Validated 10 molecules using 1 model in 1 PDB entry Analyzed V Complete Structure Wrong Chlfallty Wrong chirality (Carboni Correct cmrairiy Atom Substitution Foreign Atom 0 l0 20 30 40 SO 60 70 SO 90 TOO ‘ii of residues CSV : n . :§‘, eg: '-BE . r:» 3: -25513 5:». — 5:~i. =.: :n 3»; 2'i: i.' L5-2‘, 'i: — : :~ n. -,2 J§| 3 15:3 22014 David Senna‘ There are 10 NAG molecules in 3D12 entry and ~ 30% of them exhibit chirality issues. Let us get into more details by clicking Summary tab.
  8. 8. EJSON '¢i. —. . _ii‘. ri- Civervier. Summary Zietais NAG l nganaixpci 3:39 r. 'i: i_o O C Analyzed 7§ / 3 01 C7 Lcvnulete StrLl(tiJ'e ' I Wrong C’lI'alllv ZC1 _‘N2 05 C2 ‘mcitg Cliirality i:3.'bCil‘i | l : C’fE(X’: ’iI'alllV > / C3‘ , , r C6 94 03 Arum : ~tlD)(l(U( on ' : Foreign Atom ' O6 O4 . l -L 6 SC iClU '—»: itie: ldue: CZ»: Incomplete Structure Complete Structure Correct Ciiirality Mining Only Atoms Mining Ring: Degenerate (T I Q Wrong Ciiirality Atom Substitution Foreign Alon: Different Naming o erim in‘, ill! 3 r chirality Errors in J maleculels) A summary validation report is available for all the NAG molecules within 3D12 entry.
  9. 9. EJSON '¢i. —. . .iiii. ri- Civervler. Summary Zletals NAG l , igana: xpc. r 3:39 l. 'i: i_o Analyzed 7§ / 3 01 C7 Lcvnulete Srruuure ' I WV0i’lgC’lI'alltv ZC1 _‘N2 05 C2 iticng Clllléllty l:3.'l3C‘l‘l I I : C’fE(I’: ’iI'alllv > / C3‘ . g r C6 94 03 Arum : ~tlD)(l(U( on I : Foreign Atom ' O6 O4 7 . Q -l D 6 4 S C l Cl 0 '—»: itie: ldue: i: Incomplete Structure Complete Structure Correct Ciiirality Mining Only Atoms Mining Ring: Degenerate (T I Q Wrong Ciiirality Atom Substitution Foreign Alon: Different Naming o erim . ir. lII l chirality Errors in J lllfllecnlels) All the NAG molecules in 3Dl2 are complete.
  10. 10. Validator°3 -JS°~ Search - 3Dl2 | NAG Overview Summary Details NAG [ Liganaexpo i PDBQ i MOLO] [ 10 molecules in 1 PDB entry] B [C3Hr5NO5l n—acetylo—glucosanline] [CrliralAt0ms 15) C1 C2 C3 C4 C5 ][ Experimental Coordinates] T °7§ /38 O1 C7 WrongCiiira| ity — / C1 ‘N2 05 c2 Wrong Chiralirytcarbonl — I I . . c c °°"= ='°""a'“v — / 5 3 / C6 C4 03 A‘°m5"'m"'i°" — I 5 Foreign Amni 05 O4 0 2o 40 so 80 I00 “/6 of residues CSV Inoorrolehc structure Corrplete Structure Mining Onty Atorru lining Ring: Degenerate ‘‘ Atom Sutzmtutiolr Forefiui Atom Diiferent Naming mimi 60.0-/ ,2 Ciihlity Errors in 3 rrmlewlqs) C11DOD‘t C2 3'4. However, 3 out of l0 complete molecules exhibit chirality issue on Cl or C2 carbon. 01 1oo. ir/ ._ 10
  11. 11. Validator°3 -JS°~ Search - 3D12 | NAG Overview Summary NAG [ LIgandExpO i PDBQ i MOLQ] [ 10 molecuies In 1 PDB entry] n [C3H15NO5i n—acety| d—g| ucosamIne] [Cmra| AIOms15i C1 C2 C3 C4 C5 ][ Experirnentai Coordinates] Analyzed °7§ / Ca 01 C7 Complete Structure ' I Wrcmgchirality ‘ /51 ‘‘N2 05 c2 Wrong Chnralityicarbom ‘ I l °°"e= '°""a'"v — / C5 / C3‘ C6 C4 03 A‘°m5"'m"‘i°" — I 5 F°'*i9"A‘°"' Os 54 O 20 40 60 80 I00 “/6 of residues CSV Inoonolele Structure Conuleu Stmciure Finally, 6 of them contain substitution and i0 molecules contain atoms with unconventional atom annotation. You can inspect results into higher detail on the Details tab. Chiratity Errors in :4 nmleeulqs) subnimtiom in s moleculelsj o1 1oo. o-/ ,5 C2 313*. ‘ 01100.0‘/ ._1o
  12. 12. Validator°3 "50" Search - 3D12 | NAG Overview Summary Details NAG (10® All Motifs in 10 molecules. 1 PDB entries V @ Filter Id iiiqiil Molecule i123 A or A; 8 n Id Vaidated Mobule KR Al Mnlembs 3d12_0_0005 NAG 1138 A 2 ASN 306 A. NAG 1138 A 3d12_1_0019 NAG1I39A 2 NAG 1138A‘NAG 1139A 3d12_5_0149 NAG 1210 A 2 ASN 378 A. NAG 1210 A 3d12_6_0163 NAG 1313 A 2 ASN 481 A. NAG 1313 A 3d12_7_0177 NAG 1314 A 2 NAG 1313 A‘NAG 1314 A 3d12_15_9246 NAG 1238 D 2 ASN 306 D, NAG 1238 D 3d12_16_9260 NAG 1239 D 2 NAG 1238 D. NAG 1239 D 3d12_20_9390 NAG 1310 D 2 ASN 378 D, NAG I310 D 3d12_21_9404 NAG 1413 D 2 ASN 481 D, NAG 1413 D 3d12_22_94I8 NAG 1414 D 2 NAG 1413 D. NAG1414 D @2014 David Sehnal You can either select a whole class of issues from the drop down list, or filter all the validated molecules based on a parent PDB or Residue ID.
  13. 13. IJSON Guide Wiki Manual Search — 3D12 | NAG Overview Summary Details NAG (10) V All Moms in 10 molecules. 1 PDB entries V E Filter Id (ttqni Molecule (123 A or Al 8 n H All Moms in 10 molecules. 1 PDB entries M ‘ 3a12_n_si)o5 Complete Structure in 10 molecules. 1 PDB entries ASN 306 A, NAG 1138A » Correct Chirallly in 7 molecules, 1 PDB entries 3‘“2-'-’""9 » Correct chirality (Tolerant) in 7 molecules, 1 PDB entries ""3 ‘”‘”‘v”“‘3 1”“ sa12_5_9149 ASN 3711 , NAG 1210A 1' ifiiriiialitv in 3. i'i1iJlei: ii| es 1 PDB E'l11l| 5 sa12_s_s1s3 _ ASN 431 , NAG1313A aa12_7_s177 G, , NAG 1:113 A, NAG1314 A » Substitutions in 6 molecules. 1 PDB entries 3¢1Z_15_9245 » Foreign Atoms in 10 molecules. 1 PDB entries ASN 306 D1NAG1233D 3‘“2'16'92m chirality Error on C1 in 3 molecules, 1 PDB entries NAG 12” “NAG ‘ZED aa12_2o_939o chirality Error on C2 in 1 molecules. 1 PDB entries ASN 3711 D, NAG moo Substitution on Atom O1 in 6 molecules, 1 PDB entries “'2-2‘-91”‘ Foreign Atom 01 in 10 molecules. 1 PDB entries A5" “‘ °v"‘‘° "'39 aa12_22_941s NAG 1414 D 2 NAG 1413 D. NAG 1414 D © 2014 David Sennal Take a look at errors in chirality.
  14. 14. Validator°B -JS°~ Search — 3D12 | NAG Overview Summary Details NAG (10) V n Wrong chirality 1n 3 molecules. 1 PDB entries V E V Filter Id (1tqn) Molecule (123 A or Al 8 n > Viliad Mnleule #R Alflobotlss ISIS! Mona NAG 1314A 2 NAG1313A, NAG 1314A 1 C‘I: C1C91T7 '1 _ "v1' NAG 1413D 2 ASN 481 D, NAG 1413D 2 C1181 C9404,C2:C2C9405 3d12_22_9418 NAG 1414 D 2 MAG 1413 D, NAG 1414 D 1 C1: 81 C 9418 @2014 David Sehnal For inspecting single molecule report click any molecule. ..
  15. 15. 3o12_7_9177 (NAG) Validated l. li3'. l" Validated Molecule Missing Atoms O I Different Atom Names 0 NAG 131-1 A None None Molecules in Input Motif Missing Rings 0 I Foreign Atoms 1 NAG1313ANAG131-1A None Model Motif chirality Errors 1 M°de| |nf° o1 o4o9173 NAG 1313A NAG [ CBHGNO5] Model Mom I Substitutions 0 i’1,—3C‘€IVii‘—E1—g‘LICOS3l‘TiYlE‘ C1 C1 5 9177 None Coordinates — EXpEFll‘1€D1al Chiral Atoms i: '>i — C1 C2 C3 C-1 C5 LigandExpo 1 P08 9 1 MOL e Motif Info inniii em ii-mm , Drill cal inns You can select different visualization modes tor both the model and ya iddted molecule.
  16. 16. 3o12_7_9177 (NAG) Validated H “'i'' ’ iisiiam’. .-V input i. io: i‘ ifodel Suerir‘1:iosei1l. iodeland in iu' -- Superimposeo el and Validated Validated Molecule Missing Atoms O I Different Atom Names 0 NAG 131-1 A None None Molecules in Input Motif Missing Rings 0 I Foreign Atoms 1 NAG1313ANAG131-1A None Model Motif chirality Errors 1 M°de| |nf° o1 o4o9173 NAG 1313A NAG [ L351-“N135 ] Model Motif i’1,—3C‘€IVii‘—E1—g‘LICOS3l‘TiYlE‘ C1 C1 5 9177 Coordinates — Experimental Chiral Atoms 151 — C1 C2 C3 C-1 C5 LigandExpo i P08 9 i MOL 9 I Substitutions 0 None Motif Info inniii em ii-mm , Drtn Gui info Ditfererit structures to be visualized are a so available. Try out the superimposition of the validated molecu e and the model.
  17. 17. Validator°B 4 K / y‘. » ‘ 3o12_7_9177 (NAG) Superumposeomooelano V: v A xt _. ' Model T Missing Atoms O Validated Molecule NAG 131-1 A None Molecules in Input Motif l". Missing Rings 0 NAG1313ANAG131-1A None Model Info chirality Errors 1 NAe1c31-1,5No61 Model Motif nvacezy1‘-d-g‘; /oosarrtcne C1 C1 1: 9177 Coordinates - Experimental ChlralA1oms15l~ C1 C2 C3 C4 C5 LlganoE><po 1 P35 ©| l,1OL 9 Motif Info inmn qmirmrp DFXFI Q1 mm §JSON CW1’. .-4-. iv<: 07 C Z 8 / c1 . -“‘N2 T5 ('32 C C C’ 5c/ 3N0 I6 :4 3 06 5 4 Different Atom Names 0 None f‘ Foreign Atoms 1 Model Motif 01 0409173 NAG1313/‘« ", Substitutions O NO| 'l€ All the possible issues for the particular molecule are higlighted. Note the chirality error at Cl atom.

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