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VcJ| idcJ’rorDB

Step-by-s’rep guide
I.  I'm looking for The volidoiion resuls for specific | igcInd(s) in o porficulor PDB entry or
entries
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Database of validation results for ligands and non-standard residues in the Protein Data B...
ide First Time User Wiki Manual

Validator°3

Database of validation results for ligands and non-standard residues in the ...
9 Guide First Time User VWKI Manual
Database of validation results for ligands and non-standard residues in the Protein Da...
9 Gulde FlrstTlme User VWKI Manual
Database of validation results for ligands and non-standard residues in the Protein Dat...
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Search - 3D12 (1362 A)

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ValidatorDB: Search by Molecule Identifier

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

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ValidatorDB: Search by Molecule Identifier

  1. 1. VcJ| idcJ’rorDB Step-by-s’rep guide
  2. 2. I. I'm looking for The volidoiion resuls for specific | igcInd(s) in o porficulor PDB entry or entries
  3. 3. ,. First T me V‘. /iKiMai1LJ8 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 rnoiewies deemed relevant tor valdation are al hgands and non-standard residues wnh reasonable size [more than SIX heavy atoms) Standard ammo aads and nucleotides are not covered The vaidation is performed agailst models from wwPDE Chemical Component Dictionary (wwPDB 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 User? Check out the First Time User Hosentotion. X @2014 David Sehnal Click the Search fob. ..
  4. 4. ide First Time User Wiki Manual Validator°3 Database of validation results for ligands and non-standard residues in the Protein Data Bank. Database last updated 16I10I2014: 104126 entries from PDB org. 243597 molecules relevantforvalidafion, 17991 models from wwPDB (:00 The molecules deemed relevant for validation are all hgands and non-standard residues with reasonable size Imore than SX heavy atomsi Standard amino acids and nucleotides are not covered The validation IS performed agalist models from WWPDB cneniicai Component Dictionary IWWPDB ccoi The database IS updated weekly Quick Help Samples Search Overview Details by Molecule Details by PDB Entry Search by PDB Entry Molecule Annotation PDB Entry and Molecule Annotation Valdaholl results for selected molecules @2014 David Sehhal Select the criterion Search by Molecule Identifier.
  5. 5. 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 entriestrom PDB org. 243597 molecules relevanttorvalioation. 17937 models from wwPDB (:60 The molecules deemed relevant (or validation are all bgands and non-standard residues with reasonable size more than SIX heavy atomsi Standard amino acids and nucleotides are not covered The validation IS pervormed aganst models vroni VNIPDB Chemical Component Dictionary IWWPDB ccoi The database IS updated weekly Quick Help Samples Search Overview Details by Molecule Details by PDB Entry Search by PDB Entry Molecule Annotation PDB Entry and Molecule Annotation Search by Molecule Identifier o e: -ampiei sxamiiiez Validation FESLIIKS TOT selected lllO| €CUl€S Molecule Identifiers eg 3D12 1362A Alist otPDB entrylmolecule identifiers, chain identifier is case sensitive. separated by a newline or a comma (eg. 3312: 1362 at). 0 Enter some molecule identifiers I In New Tab Request up to 10 items to get instantaneous results [Ql. l|d( Search). Larger searches might take several milutes to complete [Slow Search]. ® 2014 David Sehnal Fill in your molecules of interest defined by the syntax <<PdblD: Residue| D Chain>>, and separate them with either a comma or a new line. The capitalization of PDB entry does not matter. Note that more molecules in a given PDB entry can be separated by a semicolon. As shown in Example 2.
  6. 6. 9 Gulde FlrstTlme User VWKI Manual Database of validation results for ligands and non-standard residues in the Protein Data Bank. Database last updated 16/10/2014: 104128 entries from PDB org. 243597 molecules relevanttorvalidafion. 17997 models from wwPDB CCD Tiie nieleciiles deemed lelewanttol Validation are all llgands and nonstandard lesldues i-ntii reasonable sl: e iniore than si- iieai~, - atomsi Standard amino atlas and nucleotides are not covered riie valldatlon is perroinied against nlodels rioni i-n-inns ciieniicai Component Dictionary ll‘/ WPDB ccoi Tiie database 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 Annotation Search by Molecule Identifier Q) Vallijrlllflll lC‘SLil'S Til ‘3Clt: “: ‘iCll: ‘l: l,llC‘S Molecule Identifiers l cli'i, —lcij 3D12 1362A A list of PDB entrylrnolecule identifiers chain identifier is case sensitive. separated by a newline or a comma (e g 3312: 1362 Al O El 2014 David Selirlal Let's keep things simple for now and click Example 1. We are interested in the validation results for the molecule identified by residue ID 1362 from chain A of PDB entry 3Dl2. Click Search. Please note that capitalization of the chain matters!
  7. 7. Va| idator°B 'J~°»°~ Search - 3D12 (1362 A) OverviewDetaiIs Validated 1 molecule, usiig 1 model, it 1 PDB entry. Analyzed Complete Slrutlure Wrong Chiraliry Wrong Chirality (Carbon) Foreign Atom 0 IO 20 30 40 50 60 70 80 90 I00 % of residues C 2 Onty calegones with at least 0 5% representation are snown Use the csv rm In View all date @2014 David Sehnal At first you can see the Overview vcilidcition results for the molecules of interest. The Summary tab contains annotation-based validation reports. In this case, the results for only one molecule were requested.
  8. 8. EJSON '¢i. —. . .i. i.i. - " i‘ . '-, ‘"ri7 ‘ 7 Civervier. Summary Zietais NGA ugandixpci 3339 i. ‘i': i_9 O C Anaiyzea O1 7§C7/ 8 l I / C1 . .‘N2 Zcwiplere Srrucluve 05 C2 Wrong C'ii'alitv | l C C Wiciig Ciiiiality i: a'bCii‘i C’ 5CZ 3‘0 ' 6 ‘4 3 Foreign Atom ’ Q (L A summary validation report is available for your selection — just a single ligand 3D12: 1362 A. Incomplete Structure Complete Structure Correct Cnirality Mining Only Atoms Mining Ring: Degenerate Wrong Ctiirality Atom Substitution Foreign Aron: Different Naming (Tolerant) . . Lg‘. Cnirality Error: III 1 iiioleculelsl Foreign Atoms in I muleculelsl ; .r ', ;i
  9. 9. Validator°3 -J30" Search - 3D12 (1362 A) Overview Summary Details NGA [ LigandExpo | PDBO | MOLQ] [ 1 molecule in1 PDB entry _] n [C3H15NO5[ChIIE| Al0l'nS(5) C1.C2.C3_C4.C5][Expenmenta| C0ordina1es] O C 7 8 Analyzed § / 01 C7 Complete Slrutlure [C1 «‘N2 05 c2 WW — | | Wrong Chirallty (Carbon) $6 E4 3 Foreign Atom 05 04 0 20 40 60 80 I00 % of residues CSV lnoonulete Stvuctiue Conplete Stlucture — *°°v°*‘ Conedchilfity lining Only Alon: lining Ring: Deaunuih ‘T I’ Wrong Chilfity Alum n Favstn Albm Diferemflarnlrig olenn Cllhllly Enou in I iiiuluailqsj C1100.0‘r. ' C21D0.O‘4.' C3100.0‘r. ' C41000‘! .' It is n-acetyl-d-galactosamine and it is complete. @2014 David Sehnal
  10. 10. EJSON '¢i. —. . .i. i.ii- -3711? ' ‘: l‘i‘E‘i‘ul€. ’. Summary Zietais NGA Jgandixpci 3339 i. ‘i': i_9 7 Anaiyzeo § / Zcwipleie Structure 05 C2 iirong C’lI'alltv | l C C 5 3 iiiciig Ci”ilr.1li[yi: é.'bCil‘i C’ CZ ‘O ' 6 ‘4 3 Foreign Aiom i 06 04 . 1 -L 6 SC iCiU '—»: itie: idue: i: Incomplete Structure Complete Structure Comect Ctiirality Mining Only Atoms Mining Ring: Degenerate (T | Wrong chirality Atom Substitution Foreign Atom Different Naming o i . i_, ,., ;. oreign A Omsinlmuleculelsl However, it exhibits wrong chirality on all carbon atoms of the sugar moiety.
  11. 11. EJSON '¢i. —. . .i. i.ii- 1"-ti‘ sf» 1 Z. i: ivervie. i. Summary - ® NGA Jgandixpci 3339 i. ‘i': i_9 O C Analyzed O 7%: / 8 ii I’ Zcwiplete Str :1 ire U K / C1 . .‘N2 iirong C’lI'alltv | l C C ‘t’viCl1gCl]lr.1li[yi: a'bCii‘i C’ 5CZ 3‘0 6 4 3 l I You can inspect any category of results by clicking Details tab. Alternativelly, you can click the appropriate bar in the plot or on the appropriate category in the table below. Since we have just a single residue clicking any of them will Comect Ctiirality Mining Only Atoms Mining Ring: Degenerate (T Wrong chirality Atom Substitution Foreign Atom Different Naming o . l'l§lE? | Lg‘. Foreign Atoms III I iiiulecuielsl chirality Error: III I maleI: ule[§) -. r ', ;i
  12. 12. Validator°3 -JS°~ Search - 3D12 (1362 A) Overview Summary Details NGA (1) v )) Wrong Cnirality in 1 molecules. 1 PDB entries V E v Filter Id (ttqni Molecule (123 A or A] 8 n Id Vaiiatodmoloiale IR Aiming: Inns Atoms NcAi3s2A 2 LXZ1361 A. NGAI362A 5 C‘I: C1C9091,C2:CZC9092.C2I: C3C9093,. . © 2014 David Sennal take us to the details page, where you can inspect single molecule validation reports.
  13. 13. 3D12_9_9091 (NGA) Valir1ateiji. ii3'. i" Validated Molecule NGA 1362 A Molecules in Input Motif LXZ1361ANGA1362 A Model Info N(3A[ C5H15NO5] ii—aceiAi i‘—d—ga ‘a crosam "79 Coordinates — Experimental Cnira| Ator‘1si5i— C1 C2 C3 C-1 C5 L1gandExpo i P08 9 ] MOL 9 Missing Atoms 0 None Missing Rings 0 None chirality Errors 5 Model C1 C2 C3 Motif C1 C 9091 C2 C 9092 C3 C 9093 im i~ rmrii You can select ditiererit visualization modes tor both the I Different Atom Names 0 None I Foreign Atoms 1 Model Motif 01 0409087 l_XZ1Z61A I Substitutions 0 None model and a validated molecule.
  14. 14. £JSON 6'17’. . 4 _ W/ allaaxen 1.10:1’ A xt ,1 Llooel v A :2 , ' O C Validated mow 7§ / 3 lnpul Moti‘ 01 C7 lulooel ' | SL1 Bill‘? 0590 MOd€l and W1 LII 7 ' ' / c1 . -“‘N2 T5 ('32 A c c . ' . , I 5 X 3‘ . ..» . ('26 C4 03 06 O4 validated Molecule F Missing Atoms 0 Different Atom Names 0 NGA 1362 A None None Molecules in Input Motif F Missing Rings 0 f‘ Foreign Atoms 1 LXZ 1361 ANGA 1362A Ngrne I‘ E _ Model Mom, Model Info "a "y "M5 D 01 04 o 9087 l_XZ1361A NGA [ cal-1,5No6] Model Motif , _ V V ‘ , substitutions 0 nvacezy1-o-galacrosamne C1 C1 C 9091 Coordinates - Experimental None _ _ c2 02 c 9092 Ch1ralAIoms 131 ~ 01 C2 C3 C4 C: V) g 5 LlganoE><po[P3E3©|1,10l_9 ‘N L3 ‘r9093 1 D 4 F‘ D Q 4 Different structures to be visualized ore dlso ovdildble. Try out the superimposition of the volidoted molecule and the model.
  15. 15. £JSON 6'11’. . K 4,. ‘ 3o12_9_9o91 (NGA) o Su0er11~1p0seo1.10oelano V; v A xt _. ’ model v A xx , ’ Validated Molecule l". Missing Atoms O ' Different Atom Names 0 NGA 1362 A None None Molecules in Input Motif F Missing Rings 0 f‘ Foreign Atoms 1 LXZ 1361 ANGA 1362A Ngrne IV E _ Model Mom, Model Info "a "y "M5 D 01 0.1 o 9087 l_XZ1361A N(3A1c31-1,511o61 Model Motif , _ V V 1 , substitutions 0 11—acet11-o-galactosa1nv1e C1 C1 1: 9091 Coordmates - Experimental None _ _ c 02 c 9092 Ch1ralAtoms1:>‘1~C1 C2 C3 C4 C3 9 V L1gan1jE><po1P: lE3©| l,1OL9 33 “W93 C4 C 9094 Motif Info 9 _ V _ lnput structure - PDB 91 W0 "° [7 909° All the possible issues for the pdrticuldr molecule ore highlighted. Note the chirdlity error at Ci-C5 carbons in the sugar moiety.

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