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Ligand identification using electron-density map correlations.

Terwilliger TC, Adams PD, Moriarty NW, Cohn JD - Acta Crystallogr. D Biol. Crystallogr. (2006)

Bottom Line: The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance.The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank.This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.

View Article: PubMed Central - HTML - PubMed

Affiliation: Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F(o) - F(c))exp(i(phi)c) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.

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(a) ATP fitted into model 2.5 Å density for ATP. (b) ddATP fitted into model density for ATP. (c) GTP fitted into model density for ATP.
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fig1: (a) ATP fitted into model 2.5 Å density for ATP. (b) ddATP fitted into model density for ATP. (c) GTP fitted into model density for ATP.

Mentions: Many of the most common ligands in the PDB are quite similar to each other. For example, the nucleotides ATP, ddATP and GTP are all highly similar in shape (Fig. 1 ▶). In order to develop a set of ligands that has less redundancy, the most common 200 ligands from the PDB were clustered based on how well each ligand could be fitted into density for another, as described in §2. Clustering in this way with a correlation coefficient threshold of 0.85 yielded 119 unique ligands, with clusters having between one and 18 members. Clustering with a threshold of 0.75 yielded 31 unique ligands, with clusters having between one and 110 members.


Ligand identification using electron-density map correlations.

Terwilliger TC, Adams PD, Moriarty NW, Cohn JD - Acta Crystallogr. D Biol. Crystallogr. (2006)

(a) ATP fitted into model 2.5 Å density for ATP. (b) ddATP fitted into model density for ATP. (c) GTP fitted into model density for ATP.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483487&req=5

fig1: (a) ATP fitted into model 2.5 Å density for ATP. (b) ddATP fitted into model density for ATP. (c) GTP fitted into model density for ATP.
Mentions: Many of the most common ligands in the PDB are quite similar to each other. For example, the nucleotides ATP, ddATP and GTP are all highly similar in shape (Fig. 1 ▶). In order to develop a set of ligands that has less redundancy, the most common 200 ligands from the PDB were clustered based on how well each ligand could be fitted into density for another, as described in §2. Clustering in this way with a correlation coefficient threshold of 0.85 yielded 119 unique ligands, with clusters having between one and 18 members. Clustering with a threshold of 0.75 yielded 31 unique ligands, with clusters having between one and 110 members.

Bottom Line: The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance.The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank.This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.

View Article: PubMed Central - HTML - PubMed

Affiliation: Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F(o) - F(c))exp(i(phi)c) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.

Show MeSH