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. 2015 Jan;43(Database issue):D465-9.
doi: 10.1093/nar/gku1088. Epub 2014 Nov 6.

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

Aqeel Ahmed  1 , Richard D Smith  1 , Jordan J Clark  1 , James B Dunbar Jr  1 , Heather A Carlson  2
Affiliations

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

Aqeel Ahmed et al. Nucleic Acids Res. 2015 Jan.

Abstract

For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. 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. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users.

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Figures

Figure 1.
Figure 1.
The new Binding MOAD scheme showing page flow and related functionalities in terms of retrieving data from the web interface. An integrated approach allowed the addition of selective downloads based on queries.
Figure 2.
Figure 2.
A screenshot of Binding MOAD's new record page for PDB ID: 3ERK. The sidebar provides the related links for navigation, external websites and downloads. The main page contains the data organized in different tables/sections. Receptor and Ligand tables are expanded by default, whereas Jmol molecular viewer and 90% family table are collapsed by default.
Figure 3.
Figure 3.
A screenshot of the browse/search listing page showing an example of filtered results based on class/subclass (Hydrolases; EC: 3.4.*.*), redundancy (leaders only), binding data range (pico to micro Molar), pdb resolutions (0.9–2 Å) and molecular weights for ligand (<800 Da).
Figure 4.
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.
See this image and copyright information in PMC

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