Limits...
Binding MOAD, a high-quality protein-ligand database.

Benson ML, Smith RD, Khazanov NA, Dimcheff B, Beaver J, Dresslar P, Nerothin J, Carlson HA - Nucleic Acids Res. (2007)

Bottom Line: Several technologies, such as natural language processing, help drive this constant expansion.The website now showcases a faster, more featured viewer to examine the protein-ligand structures.Ligands have additional chemical data, allowing for cheminformatics mining.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Graduate Program, Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, Torrey Path LLC, Ann Arbor, MI 48104, USA.

ABSTRACT
Binding MOAD (Mother of All Databases) is a database of 9836 protein-ligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has improved usability. The website now showcases a faster, more featured viewer to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. Lastly, logins are no longer necessary, and Binding MOAD is freely available to all at http://www.BindingMOAD.org.

Show MeSH
Distribution of binding affinities in Binding MOAD. Data is labeled as Kd (blue), IC50 (yellow) and Ki (red). For this figure, binding affinities were simply converted to free energies by RT × ln(affinity). While this conversion not strictly appropriate for Ki or IC50, it provides a comparison for the reader.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238910&req=5

Figure 1: Distribution of binding affinities in Binding MOAD. Data is labeled as Kd (blue), IC50 (yellow) and Ki (red). For this figure, binding affinities were simply converted to free energies by RT × ln(affinity). While this conversion not strictly appropriate for Ki or IC50, it provides a comparison for the reader.

Mentions: Binding MOAD is constructed with a top-down approach, starting with all entries in the PDB (18) and eliminating structures which are inappropriate. This is more efficient than a ground-up approach of reading the literature as a whole to identify appropriate complexes. Each entry in Binding MOAD must have resolution better than 2.5 Å, and each entry must contain a valid ligand. Valid ligands are biologically relevant small molecules and can include agonists, antagonists, cofactors, inhibitors, allosteric regulators, enzymatic products, etc. Covalently attached molecules (covalent inhibitors or posttranslational modifications to the protein) are not considered valid ligands. The focus is proteins binding small molecules, so peptides larger than 10 amino acids and chains of greater than four nucleic acids are not considered valid ligands. Many small molecules present in a crystal structure are not considered biologically relevant because they are part of the crystallization matrix and an artifact of the protein in an artificial condensed phase. Such molecules include solvents, buffers, detergents and salts, but care must be taken because some small molecules are valid ligands in some structures but additives in others. Examples of such are sugars, membrane components, small organic molecules (e.g. toluene) and metabolites (e.g. citrate). Figures 1 and 2 illustrate the wide distribution of data available in Binding MOAD, in terms of binding affinity and size, respectively.Figure 1.


Binding MOAD, a high-quality protein-ligand database.

Benson ML, Smith RD, Khazanov NA, Dimcheff B, Beaver J, Dresslar P, Nerothin J, Carlson HA - Nucleic Acids Res. (2007)

Distribution of binding affinities in Binding MOAD. Data is labeled as Kd (blue), IC50 (yellow) and Ki (red). For this figure, binding affinities were simply converted to free energies by RT × ln(affinity). While this conversion not strictly appropriate for Ki or IC50, it provides a comparison for the reader.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238910&req=5

Figure 1: Distribution of binding affinities in Binding MOAD. Data is labeled as Kd (blue), IC50 (yellow) and Ki (red). For this figure, binding affinities were simply converted to free energies by RT × ln(affinity). While this conversion not strictly appropriate for Ki or IC50, it provides a comparison for the reader.
Mentions: Binding MOAD is constructed with a top-down approach, starting with all entries in the PDB (18) and eliminating structures which are inappropriate. This is more efficient than a ground-up approach of reading the literature as a whole to identify appropriate complexes. Each entry in Binding MOAD must have resolution better than 2.5 Å, and each entry must contain a valid ligand. Valid ligands are biologically relevant small molecules and can include agonists, antagonists, cofactors, inhibitors, allosteric regulators, enzymatic products, etc. Covalently attached molecules (covalent inhibitors or posttranslational modifications to the protein) are not considered valid ligands. The focus is proteins binding small molecules, so peptides larger than 10 amino acids and chains of greater than four nucleic acids are not considered valid ligands. Many small molecules present in a crystal structure are not considered biologically relevant because they are part of the crystallization matrix and an artifact of the protein in an artificial condensed phase. Such molecules include solvents, buffers, detergents and salts, but care must be taken because some small molecules are valid ligands in some structures but additives in others. Examples of such are sugars, membrane components, small organic molecules (e.g. toluene) and metabolites (e.g. citrate). Figures 1 and 2 illustrate the wide distribution of data available in Binding MOAD, in terms of binding affinity and size, respectively.Figure 1.

Bottom Line: Several technologies, such as natural language processing, help drive this constant expansion.The website now showcases a faster, more featured viewer to examine the protein-ligand structures.Ligands have additional chemical data, allowing for cheminformatics mining.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Graduate Program, Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, Torrey Path LLC, Ann Arbor, MI 48104, USA.

ABSTRACT
Binding MOAD (Mother of All Databases) is a database of 9836 protein-ligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has improved usability. The website now showcases a faster, more featured viewer to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. Lastly, logins are no longer necessary, and Binding MOAD is freely available to all at http://www.BindingMOAD.org.

Show MeSH