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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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Flowchart and results of automatic ligand building for 2663 entries with ligands that contain more than six non-H atoms, 706 small ligands with five or six atoms and 1194 ‘good’ ligands. The sites for large ligands are easier to locate, but it is more difficult to construct them.
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fig5: Flowchart and results of automatic ligand building for 2663 entries with ligands that contain more than six non-H atoms, 706 small ligands with five or six atoms and 1194 ‘good’ ligands. The sites for large ligands are easier to locate, but it is more difficult to construct them.

Mentions: An overall assessment of the performance of the procedure along the pipeline of building steps is shown in Fig. 5 ▶. Large ligands are built in 27% of cases and small ones in 31% of cases.


Assessment of automatic ligand building in ARP/wARP.

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

Flowchart and results of automatic ligand building for 2663 entries with ligands that contain more than six non-H atoms, 706 small ligands with five or six atoms and 1194 ‘good’ ligands. The sites for large ligands are easier to locate, but it is more difficult to construct them.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: Flowchart and results of automatic ligand building for 2663 entries with ligands that contain more than six non-H atoms, 706 small ligands with five or six atoms and 1194 ‘good’ ligands. The sites for large ligands are easier to locate, but it is more difficult to construct them.
Mentions: An overall assessment of the performance of the procedure along the pipeline of building steps is shown in Fig. 5 ▶. Large ligands are built in 27% of cases and small ones in 31% of cases.

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