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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
EolasViewer for 3ERK. The SB4 ligand is shown in ball in stick inside the pocket. The surfaces shown are the ligand surface in blue, the binding site in red and the solvent-exposed regions of the binding site are in green. (Top) The protein backbone is shown as a gray ribbon, and in the close-up (Bottom), the backbone is colored by B-factors.
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Figure 4: EolasViewer for 3ERK. The SB4 ligand is shown in ball in stick inside the pocket. The surfaces shown are the ligand surface in blue, the binding site in red and the solvent-exposed regions of the binding site are in green. (Top) The protein backbone is shown as a gray ribbon, and in the close-up (Bottom), the backbone is colored by B-factors.

Mentions: The greatest improvement comes as a new tool for viewing the complex in 3D. The GoCavViewer has been replaced by the EolasViewer; screenshot of the viewer is shown in Figure 4. As before, the viewer is capable of displaying the ligand pocket using both ball-stick and surface representations; the surfaces come from our code GoCAV which was specifically developed for Binding MOAD (19). However, EolasViewer incorporates significant improvements in the areas of performance, visual quality and back-end flexibility for future application development efforts.Figure 4.


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)

EolasViewer for 3ERK. The SB4 ligand is shown in ball in stick inside the pocket. The surfaces shown are the ligand surface in blue, the binding site in red and the solvent-exposed regions of the binding site are in green. (Top) The protein backbone is shown as a gray ribbon, and in the close-up (Bottom), the backbone is colored by B-factors.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: EolasViewer for 3ERK. The SB4 ligand is shown in ball in stick inside the pocket. The surfaces shown are the ligand surface in blue, the binding site in red and the solvent-exposed regions of the binding site are in green. (Top) The protein backbone is shown as a gray ribbon, and in the close-up (Bottom), the backbone is colored by B-factors.
Mentions: The greatest improvement comes as a new tool for viewing the complex in 3D. The GoCavViewer has been replaced by the EolasViewer; screenshot of the viewer is shown in Figure 4. As before, the viewer is capable of displaying the ligand pocket using both ball-stick and surface representations; the surfaces come from our code GoCAV which was specifically developed for Binding MOAD (19). However, EolasViewer incorporates significant improvements in the areas of performance, visual quality and back-end flexibility for future application development efforts.Figure 4.

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