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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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Related in: MedlinePlus

Distribution of r.m.s.d. values between the reconstructed and the reference ligand. The plot highlights the three different regions: 1.0 Å and below, correctly built ligand in correctly identified site; between 1.0 Å and 10 Å, the ligand is at a correct site but not properly built; above 10 Å, the ligand is built at an incorrect location.
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fig2: Distribution of r.m.s.d. values between the reconstructed and the reference ligand. The plot highlights the three different regions: 1.0 Å and below, correctly built ligand in correctly identified site; between 1.0 Å and 10 Å, the ligand is at a correct site but not properly built; above 10 Å, the ligand is built at an incorrect location.

Mentions: The distribution of the r.m.s.d. values obtained from the large-scale test exhibits three main regions (Fig. 2 ▶): (i) an interatomic scale (below 1 Å), corresponding to correctly built ligands, (ii) an intramolecular scale (between 1 and 10 Å), where the ligand was built into the correct cluster but in a wrong conformation, and (iii) the intermolecular scale (above 10 Å), where the ligand was built at an incorrect site. Therefore, cases with r.m.s.d. values of equal or less than 1.0 Å were considered to be successful reconstructions. Such a coordinate error should also be (almost) within the radius of convergence of modern refinement programs.


Assessment of automatic ligand building in ARP/wARP.

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

Distribution of r.m.s.d. values between the reconstructed and the reference ligand. The plot highlights the three different regions: 1.0 Å and below, correctly built ligand in correctly identified site; between 1.0 Å and 10 Å, the ligand is at a correct site but not properly built; above 10 Å, the ligand is built at an incorrect location.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Distribution of r.m.s.d. values between the reconstructed and the reference ligand. The plot highlights the three different regions: 1.0 Å and below, correctly built ligand in correctly identified site; between 1.0 Å and 10 Å, the ligand is at a correct site but not properly built; above 10 Å, the ligand is built at an incorrect location.
Mentions: The distribution of the r.m.s.d. values obtained from the large-scale test exhibits three main regions (Fig. 2 ▶): (i) an interatomic scale (below 1 Å), corresponding to correctly built ligands, (ii) an intramolecular scale (between 1 and 10 Å), where the ligand was built into the correct cluster but in a wrong conformation, and (iii) the intermolecular scale (above 10 Å), where the ligand was built at an incorrect site. Therefore, cases with r.m.s.d. values of equal or less than 1.0 Å were considered to be successful reconstructions. Such a coordinate error should also be (almost) within the radius of convergence of modern refinement programs.

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