comparing acedrg vs csd · • run refmac5 to assess geometry (idealisation mode) compare with csd...
TRANSCRIPT
AceDRG vs CSDSuggested by Oliver Smart
Monomer library update CCD entries in the CSD
323 5073 1517
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AceDRG vs CSD323 Comp IDs from the CCD
Establish Baseline – original PDB files:• Take PDBs• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
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AceDRG vs CSD323 Comp IDs from the CCD
Establish Baseline – original PDB files:• Take PDBs• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
Re-refined PDB using AceDRG dictionary (monomer library update)• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
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AceDRG vs CSD323 Comp IDs from the CCD
Establish Baseline – original PDB files:• Take PDBs• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
Re-refined PDB using AceDRG dictionary (monomer library update)• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
Compare with CSD model:• Take coordinates• Run REFMAC5 to assess geometry (idealisation mode)
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PDB ligands
REFMAC5 function value
Frequency
010
2030
4050
10 100 1000 10000
PDB ligands
REFMAC5 function value
Frequency
010
2030
4050
10 100 1000 10000
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PDB ligands
REFMAC5 function value
Frequency
010
2030
4050
10 100 1000 10000
8
PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
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DifferentnumbersofmoleculesinPDBfile.OnlyeveroneinCCD/CSDfile.Differentnumberofatomsindifferentligands.SoluGon:scalebynumberofatoms.
Mostligands(250/323)presentonce.Somearepresent2-11Gmes.3h6ihas102DMFligands.
PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
10
PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
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PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
12
ANL : 2ov47 atomsf = 3435
PDB ligands Re-Refined with AceDRG
REFMAC5 function value per atom
Frequency
020
4060
80100
0.1 1 10 100 1000
13
CSD ligands (CCD representatives)
REFMAC5 function value per atom
Frequency
020
4060
80100
0.1 1 10 100 1000
14
-0.5 0.0 0.5 1.0
-10
12
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QQ-Plot - REFMAC5 function value per atom
PDB ligands Re-Refined with AceDRG
CS
D li
gand
s (C
CD
repr
esen
tativ
es)
15
-0.5 0.0 0.5 1.0
-10
12
3
REFMAC5 function value per atom
PDB ligands Re-Refined with AceDRG
CS
D li
gand
s (C
CD
repr
esen
tativ
es)
16
-0.5 0.0 0.5 1.0
-10
12
3
REFMAC5 function value per atom
PDB ligands Re-Refined with AceDRG
CS
D li
gand
s (C
CD
repr
esen
tativ
es)
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AOM4OA1AN3C0
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AOM : 1lho
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AOM : 1lho
AOM (CSD)
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AOM : 1lho
AOM (CSD)
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AOM : 1lho
AOM (CSD)Refined 1cyc
22
4OA: 4q0a
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4OA: 4q0a
4OA (CSD)
24
4OA: 4q0a
4OA (CSD)
25
4OA: 4q0a
4OA (CSD)Refined 1cyc
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1AN: 1lgw
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1AN: 1lgw
1AN (CSD)
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1AN: 1lgw
1AN (CSD)Refined 1cyc
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3C0: 4u16
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3C0: 4u16
3C0 (CSD)
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3C0: 4u16
3C0 (CSD)
32
3C0: 4u16
3C0 (CSD)Refined 1cyc
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SummaryNotes:• LigandmaybeinaparGcularconformaGonduetoenvironment–notscoringidealconformaGons
• RidinghydrogensareaddedbyREFMACandusedforscoring.• MadeadifferenceforafeworiginalPDBentries(3AQin4txs).• Nodifferenceinre-refinedorCSDligands.
Conclusions:• ThereareproblemsintheCSDmodels.
• CouldinvesGgatefurther,andreporttoCSD.• Noteissuescouldbeinintermediatesteps–CCD,Coot,etc.
• Nomenclatureinconsistencies–howdowedealwiththis?
• NothingconcerningidenGfiedthatshouldmakeuseworriedaboutAceDRG.• Noextremeoutliersa_erre-refinementwithAceDRG.• ThereareissuesinthemodelsdepositedinthePDB(nosurprise).