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LigASite--a database of biologically relevant binding sites in proteins with known apo-structures.

Dessailly BH, Lensink MF, Orengo CA, Wodak SJ - Nucleic Acids Res. (2007)

Bottom Line: In defining the binding sites for each protein, information from all holo-structures is combined, considering in each case the quaternary structure defined by the PQS server.LigASite is built using simple criteria and is automatically updated as new structures become available in the PDB, thereby guaranteeing optimal data coverage over time.The datasets can be downloaded from the website as Schema-validated XML files or comma-separated flat files.

View Article: PubMed Central - PubMed

Affiliation: Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (U. L. B.), Bld du Triomphe - CP 263, 1050 Bruxelles, Belgium.

ABSTRACT
Better characterization of binding sites in proteins and the ability to accurately predict their location and energetic properties are major challenges which, if addressed, would have many valuable practical applications. Unfortunately, reliable benchmark datasets of binding sites in proteins are still sorely lacking. Here, we present LigASite ('LIGand Attachment SITE'), a gold-standard dataset of binding sites in 550 proteins of known structures. LigASite consists exclusively of biologically relevant binding sites in proteins for which at least one apo- and one holo-structure are available. In defining the binding sites for each protein, information from all holo-structures is combined, considering in each case the quaternary structure defined by the PQS server. LigASite is built using simple criteria and is automatically updated as new structures become available in the PDB, thereby guaranteeing optimal data coverage over time. Both a redundant and a culled non-redundant version of the dataset is available at http://www.scmbb.ulb.ac.be/Users/benoit/LigASite. The website interface allows users to search the dataset by PDB identifiers, ligand identifiers, protein names or sequence, and to look for structural matches as defined by the CATH homologous superfamilies. The datasets can be downloaded from the website as Schema-validated XML files or comma-separated flat files.

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Turkey egg-white lysozyme. (a) Mapping of binding site residues on the apo-structure (PDB entry 135l). These residues are identified as part of the binding site from the three holo-structures in which the lysozyme is in complex with different ligands: (b) with three molecules of N-acetyl-d-glucosamine (NAG) and a sulphate ion in PDB entry 1jef; (c) with di(N-acetyl-d-glucosamine) in PDB entry 1ljn; and (d) with two molecules of NAG in PDB entry 1lzy. Binding site residues are coloured red if they are in contact with ligand atoms in all three holo-structures (i.e. frequency score of 1.0 = 3/3), they are coloured orange if they are only in contact with ligand atoms in two of the holo-structures (i.e. frequency score of 0.67 ≈ 2/3), and they are coloured yellow if they are in contact with ligand atoms in only one holo-structure (i.e. frequency score of 0.33 ≈ 1/3). HET-groups considered as biologically relevant in LigASite are displayed and coloured in CPK. Sulphate ions filtered out as biologically irrelevant in PDB entry 1ljn are transparent and displayed in balls-and-sticks. The figure was drawn with molscript (27) and rendered with Raster3D (28).
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Figure 2: Turkey egg-white lysozyme. (a) Mapping of binding site residues on the apo-structure (PDB entry 135l). These residues are identified as part of the binding site from the three holo-structures in which the lysozyme is in complex with different ligands: (b) with three molecules of N-acetyl-d-glucosamine (NAG) and a sulphate ion in PDB entry 1jef; (c) with di(N-acetyl-d-glucosamine) in PDB entry 1ljn; and (d) with two molecules of NAG in PDB entry 1lzy. Binding site residues are coloured red if they are in contact with ligand atoms in all three holo-structures (i.e. frequency score of 1.0 = 3/3), they are coloured orange if they are only in contact with ligand atoms in two of the holo-structures (i.e. frequency score of 0.67 ≈ 2/3), and they are coloured yellow if they are in contact with ligand atoms in only one holo-structure (i.e. frequency score of 0.33 ≈ 1/3). HET-groups considered as biologically relevant in LigASite are displayed and coloured in CPK. Sulphate ions filtered out as biologically irrelevant in PDB entry 1ljn are transparent and displayed in balls-and-sticks. The figure was drawn with molscript (27) and rendered with Raster3D (28).

Mentions: When several holo-structures are available for a given protein, all are used to define its binding site. Many holo-structures are bound to only a portion of the natural ligands, and the picture of the binding site that is obtained when considering all available holo-structures is therefore more complete and accurate. Out of the 550 proteins in the redundant dataset, 291 have more than one holo-structure. A frequency score is assigned to all binding site residues in a protein, based on the fraction of corresponding holo-structures in which the residue is observed to be part of a biologically relevant binding site (Figure 2).Figure 2.


LigASite--a database of biologically relevant binding sites in proteins with known apo-structures.

Dessailly BH, Lensink MF, Orengo CA, Wodak SJ - Nucleic Acids Res. (2007)

Turkey egg-white lysozyme. (a) Mapping of binding site residues on the apo-structure (PDB entry 135l). These residues are identified as part of the binding site from the three holo-structures in which the lysozyme is in complex with different ligands: (b) with three molecules of N-acetyl-d-glucosamine (NAG) and a sulphate ion in PDB entry 1jef; (c) with di(N-acetyl-d-glucosamine) in PDB entry 1ljn; and (d) with two molecules of NAG in PDB entry 1lzy. Binding site residues are coloured red if they are in contact with ligand atoms in all three holo-structures (i.e. frequency score of 1.0 = 3/3), they are coloured orange if they are only in contact with ligand atoms in two of the holo-structures (i.e. frequency score of 0.67 ≈ 2/3), and they are coloured yellow if they are in contact with ligand atoms in only one holo-structure (i.e. frequency score of 0.33 ≈ 1/3). HET-groups considered as biologically relevant in LigASite are displayed and coloured in CPK. Sulphate ions filtered out as biologically irrelevant in PDB entry 1ljn are transparent and displayed in balls-and-sticks. The figure was drawn with molscript (27) and rendered with Raster3D (28).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238865&req=5

Figure 2: Turkey egg-white lysozyme. (a) Mapping of binding site residues on the apo-structure (PDB entry 135l). These residues are identified as part of the binding site from the three holo-structures in which the lysozyme is in complex with different ligands: (b) with three molecules of N-acetyl-d-glucosamine (NAG) and a sulphate ion in PDB entry 1jef; (c) with di(N-acetyl-d-glucosamine) in PDB entry 1ljn; and (d) with two molecules of NAG in PDB entry 1lzy. Binding site residues are coloured red if they are in contact with ligand atoms in all three holo-structures (i.e. frequency score of 1.0 = 3/3), they are coloured orange if they are only in contact with ligand atoms in two of the holo-structures (i.e. frequency score of 0.67 ≈ 2/3), and they are coloured yellow if they are in contact with ligand atoms in only one holo-structure (i.e. frequency score of 0.33 ≈ 1/3). HET-groups considered as biologically relevant in LigASite are displayed and coloured in CPK. Sulphate ions filtered out as biologically irrelevant in PDB entry 1ljn are transparent and displayed in balls-and-sticks. The figure was drawn with molscript (27) and rendered with Raster3D (28).
Mentions: When several holo-structures are available for a given protein, all are used to define its binding site. Many holo-structures are bound to only a portion of the natural ligands, and the picture of the binding site that is obtained when considering all available holo-structures is therefore more complete and accurate. Out of the 550 proteins in the redundant dataset, 291 have more than one holo-structure. A frequency score is assigned to all binding site residues in a protein, based on the fraction of corresponding holo-structures in which the residue is observed to be part of a biologically relevant binding site (Figure 2).Figure 2.

Bottom Line: In defining the binding sites for each protein, information from all holo-structures is combined, considering in each case the quaternary structure defined by the PQS server.LigASite is built using simple criteria and is automatically updated as new structures become available in the PDB, thereby guaranteeing optimal data coverage over time.The datasets can be downloaded from the website as Schema-validated XML files or comma-separated flat files.

View Article: PubMed Central - PubMed

Affiliation: Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (U. L. B.), Bld du Triomphe - CP 263, 1050 Bruxelles, Belgium.

ABSTRACT
Better characterization of binding sites in proteins and the ability to accurately predict their location and energetic properties are major challenges which, if addressed, would have many valuable practical applications. Unfortunately, reliable benchmark datasets of binding sites in proteins are still sorely lacking. Here, we present LigASite ('LIGand Attachment SITE'), a gold-standard dataset of binding sites in 550 proteins of known structures. LigASite consists exclusively of biologically relevant binding sites in proteins for which at least one apo- and one holo-structure are available. In defining the binding sites for each protein, information from all holo-structures is combined, considering in each case the quaternary structure defined by the PQS server. LigASite is built using simple criteria and is automatically updated as new structures become available in the PDB, thereby guaranteeing optimal data coverage over time. Both a redundant and a culled non-redundant version of the dataset is available at http://www.scmbb.ulb.ac.be/Users/benoit/LigASite. The website interface allows users to search the dataset by PDB identifiers, ligand identifiers, protein names or sequence, and to look for structural matches as defined by the CATH homologous superfamilies. The datasets can be downloaded from the website as Schema-validated XML files or comma-separated flat files.

Show MeSH