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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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Examples of density maps with different values of the real-space map correlation coefficient (RSMCC). The ligand adenosinediphosphate is shown as from the PDB entries 1in7 with an RSMCC of 93% (a) and 1hw8 with an RSMCC of 69% (b). The maps are contoured at 0.06 e Å−3 (blue) and 0.15 e Å−3 (brown).
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fig4: Examples of density maps with different values of the real-space map correlation coefficient (RSMCC). The ligand adenosinediphosphate is shown as from the PDB entries 1in7 with an RSMCC of 93% (a) and 1hw8 with an RSMCC of 69% (b). The maps are contoured at 0.06 e Å−3 (blue) and 0.15 e Å−3 (brown).

Mentions: The values of RSMCC have a sharp peak at around 0.85–0.95 corresponding to the structures where the ligand is well defined in the density. There is a long tail to the left, some possible reasons for which are elaborated in the subsequent sections. To give a visual impression on how RSMCC relates to the map quality, Fig. 4 ▶ presents an example with the PDB entries 1in7 and 1hw8, both refined at a resolution of 2.0 Å and containing a bound adenosinediphosphate molecule. While the density for RSMCC of 93% is very clear, that for RSMCC of 69% lacks experimental support and is difficult to interpret, particularly for the pyrophosphate part of the ligand.


Assessment of automatic ligand building in ARP/wARP.

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

Examples of density maps with different values of the real-space map correlation coefficient (RSMCC). The ligand adenosinediphosphate is shown as from the PDB entries 1in7 with an RSMCC of 93% (a) and 1hw8 with an RSMCC of 69% (b). The maps are contoured at 0.06 e Å−3 (blue) and 0.15 e Å−3 (brown).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Examples of density maps with different values of the real-space map correlation coefficient (RSMCC). The ligand adenosinediphosphate is shown as from the PDB entries 1in7 with an RSMCC of 93% (a) and 1hw8 with an RSMCC of 69% (b). The maps are contoured at 0.06 e Å−3 (blue) and 0.15 e Å−3 (brown).
Mentions: The values of RSMCC have a sharp peak at around 0.85–0.95 corresponding to the structures where the ligand is well defined in the density. There is a long tail to the left, some possible reasons for which are elaborated in the subsequent sections. To give a visual impression on how RSMCC relates to the map quality, Fig. 4 ▶ presents an example with the PDB entries 1in7 and 1hw8, both refined at a resolution of 2.0 Å and containing a bound adenosinediphosphate molecule. While the density for RSMCC of 93% is very clear, that for RSMCC of 69% lacks experimental support and is difficult to interpret, particularly for the pyrophosphate part of the ligand.

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