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Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

Ahmed A, Smith RD, Clark JJ, Dunbar JB, Carlson HA - Nucleic Acids Res. (2014)

Bottom Line: Currently, it contains 23,269 complexes and 8156 binding affinities.In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment.The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, University of Michigan, 428 Church St, Ann Arbor, MI 48109-1065, USA.

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A screenshot of the search page that has the additional feature for ligand-structure searching along with the previous field-based searching. Ligand structure/substructure searching is provided using JChem (17), which allows drawing the ligand structure (not shown), searching the database and displaying the results (shown). Here is an example of substructure ligand searching for Naphthalene.
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Figure 4: A screenshot of the search page that has the additional feature for ligand-structure searching along with the previous field-based searching. Ligand structure/substructure searching is provided using JChem (17), which allows drawing the ligand structure (not shown), searching the database and displaying the results (shown). Here is an example of substructure ligand searching for Naphthalene.

Mentions: In addition to the previous field-based search, we have now incorporated structure-based searching of ligands using ChemAxon tools. This allows users to search ligands very efficiently by structure (e.g. ‘Substructure’, ‘Superstructure’, ‘Similarity’ and ‘Full structure’) in Binding MOAD. Users can draw chemical structures into the embedded applet MarvinSketch that is used to search the stored Binding MOAD ligands via the JChem Base tool. The matched ligand structures resulting from the search query can be seen in MarvinView and the associated Binding MOAD records for each result can be accessed by the ‘Search MOAD records’ button, as shown in Figure 4.


Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

Ahmed A, Smith RD, Clark JJ, Dunbar JB, Carlson HA - Nucleic Acids Res. (2014)

A screenshot of the search page that has the additional feature for ligand-structure searching along with the previous field-based searching. Ligand structure/substructure searching is provided using JChem (17), which allows drawing the ligand structure (not shown), searching the database and displaying the results (shown). Here is an example of substructure ligand searching for Naphthalene.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383918&req=5

Figure 4: A screenshot of the search page that has the additional feature for ligand-structure searching along with the previous field-based searching. Ligand structure/substructure searching is provided using JChem (17), which allows drawing the ligand structure (not shown), searching the database and displaying the results (shown). Here is an example of substructure ligand searching for Naphthalene.
Mentions: In addition to the previous field-based search, we have now incorporated structure-based searching of ligands using ChemAxon tools. This allows users to search ligands very efficiently by structure (e.g. ‘Substructure’, ‘Superstructure’, ‘Similarity’ and ‘Full structure’) in Binding MOAD. Users can draw chemical structures into the embedded applet MarvinSketch that is used to search the stored Binding MOAD ligands via the JChem Base tool. The matched ligand structures resulting from the search query can be seen in MarvinView and the associated Binding MOAD records for each result can be accessed by the ‘Search MOAD records’ button, as shown in Figure 4.

Bottom Line: Currently, it contains 23,269 complexes and 8156 binding affinities.In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment.The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, University of Michigan, 428 Church St, Ann Arbor, MI 48109-1065, USA.

Show MeSH