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Assessment of automatic ligand building in ARP/wARP.

Evrard GX, Langer GG, Perrakis A, Lamzin VS - Acta Crystallogr. D Biol. Crystallogr. (2006)

Bottom Line: Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model.The first step is most successful for large ligands.Both steps are successful for ligands with low to moderate atomic displacement parameters.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany. evrard@embl-hamburg.de

ABSTRACT
The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.

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Distribution of ligand sizes (non-H atoms) for the initially selected full sample and the sample of largest ligands. Outstanding peaks reflect the presence of widespread ligands, e.g. HED, ADP, ATP, HEM, NAP, FAD for sizes 8, 27, 31, 43, 48 and 53, respectively.
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fig1: Distribution of ligand sizes (non-H atoms) for the initially selected full sample and the sample of largest ligands. Outstanding peaks reflect the presence of widespread ligands, e.g. HED, ADP, ATP, HEM, NAP, FAD for sizes 8, 27, 31, 43, 48 and 53, respectively.

Mentions: The test sample is very diverse in terms of the ligand size (Fig. 1 ▶), with the largest ligand, adeninylpentylcobalamin in PDB entry 1eex, containing 106 non-H atoms. Ligands with five or six atoms (e.g. sulfate and phosphate ions) largely outnumber other ligands and this was taken into account to avoid bias in the analysis.


Assessment of automatic ligand building in ARP/wARP.

Evrard GX, Langer GG, Perrakis A, Lamzin VS - Acta Crystallogr. D Biol. Crystallogr. (2006)

Distribution of ligand sizes (non-H atoms) for the initially selected full sample and the sample of largest ligands. Outstanding peaks reflect the presence of widespread ligands, e.g. HED, ADP, ATP, HEM, NAP, FAD for sizes 8, 27, 31, 43, 48 and 53, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483501&req=5

fig1: Distribution of ligand sizes (non-H atoms) for the initially selected full sample and the sample of largest ligands. Outstanding peaks reflect the presence of widespread ligands, e.g. HED, ADP, ATP, HEM, NAP, FAD for sizes 8, 27, 31, 43, 48 and 53, respectively.
Mentions: The test sample is very diverse in terms of the ligand size (Fig. 1 ▶), with the largest ligand, adeninylpentylcobalamin in PDB entry 1eex, containing 106 non-H atoms. Ligands with five or six atoms (e.g. sulfate and phosphate ions) largely outnumber other ligands and this was taken into account to avoid bias in the analysis.

Bottom Line: Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model.The first step is most successful for large ligands.Both steps are successful for ligands with low to moderate atomic displacement parameters.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany. evrard@embl-hamburg.de

ABSTRACT
The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.

Show MeSH
Related in: MedlinePlus