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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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Effect of the size of the ligand on the efficiency of the procedure. The total test set is in a darker colour; ‘good’ ligands are in a lighter colour.
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fig6: Effect of the size of the ligand on the efficiency of the procedure. The total test set is in a darker colour; ‘good’ ligands are in a lighter colour.

Mentions: The location of the binding site and the construction of the ligand molecule are differently affected by the size of the ligand (Fig. 6 ▶). Consistently with the intrinsic structure of the algorithm, it is easier to locate the binding sites for larger ligands, while smaller ligands are simpler to build. One reason for this is the fact that the site identification considers all possible clusters in the density by their volume. Conversely, the construction step takes into account all interpretations of a single selected cluster in terms of a ligand molecule.


Assessment of automatic ligand building in ARP/wARP.

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

Effect of the size of the ligand on the efficiency of the procedure. The total test set is in a darker colour; ‘good’ ligands are in a lighter colour.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig6: Effect of the size of the ligand on the efficiency of the procedure. The total test set is in a darker colour; ‘good’ ligands are in a lighter colour.
Mentions: The location of the binding site and the construction of the ligand molecule are differently affected by the size of the ligand (Fig. 6 ▶). Consistently with the intrinsic structure of the algorithm, it is easier to locate the binding sites for larger ligands, while smaller ligands are simpler to build. One reason for this is the fact that the site identification considers all possible clusters in the density by their volume. Conversely, the construction step takes into account all interpretations of a single selected cluster in terms of a ligand molecule.

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