Binding MOAD


25378330	Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. [PMID: 25378330] Ahmed A, Smith RD, Clark JJ, Dunbar JB, Carlson HA. 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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2015:43(Database issue) \| 43 Citations (from Europe PMC, 2025-03-29)
15971202	Binding MOAD (Mother Of All Databases). [PMID: 15971202] Hu L, Benson ML, Smith RD, Lerner MG, Carlson HA. Abstract Binding MOAD (Mother of All Databases) is the largest collection of high-quality, protein-ligand complexes available from the Protein Data Bank. At this time, Binding MOAD contains 5331 protein-ligand complexes comprised of 1780 unique protein families and 2630 unique ligands. We have searched the crystallography papers for all 5000+ structures and compiled binding data for 1375 (26%) of the protein-ligand complexes. The binding-affinity data ranges 13 orders of magnitude. This is the largest collection of binding data reported to date in the literature. We have also addressed the issue of redundancy in the data. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 "best" complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This significant collection of protein-ligand complexes will be very useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques. The dataset can be accessed at http://www.BindingMOAD.org. (c) 2005 Wiley-Liss, Inc Proteins. 2005:60(3) \| 129 Citations (from Europe PMC, 2025-03-29)

Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. [PMID: 25378330]

Ahmed A, Smith RD, Clark JJ, Dunbar JB, Carlson HA.

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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 43 Citations (from Europe PMC, 2025-03-29)

Binding MOAD (Mother Of All Databases). [PMID: 15971202]

Hu L, Benson ML, Smith RD, Lerner MG, Carlson HA.

Abstract

Binding MOAD (Mother of All Databases) is the largest collection of high-quality, protein-ligand complexes available from the Protein Data Bank. At this time, Binding MOAD contains 5331 protein-ligand complexes comprised of 1780 unique protein families and 2630 unique ligands. We have searched the crystallography papers for all 5000+ structures and compiled binding data for 1375 (26%) of the protein-ligand complexes. The binding-affinity data ranges 13 orders of magnitude. This is the largest collection of binding data reported to date in the literature. We have also addressed the issue of redundancy in the data. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 "best" complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This significant collection of protein-ligand complexes will be very useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques. The dataset can be accessed at http://www.BindingMOAD.org. (c) 2005 Wiley-Liss, Inc

Proteins. 2005:60(3) | 129 Citations (from Europe PMC, 2025-03-29)

URL:	http://www.bindingmoad.org/
Full name:	Binding Mother of All Databases
Description:	Binding MOAD is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding.
Year founded:	2005
Last update:	2013
Version:	v1.0
Accessibility:	Accessible
Country/Region:	United States

Data type:	Protein
Data object:
Database category:	Structure
Major species:
Keywords:	ligand-protein binding

University/Institution:	University of Michigan
Address:	428 Church St,Ann Arbor,MI 48109-1065,USA
City:	Ann Arbor
Province/State:	MI
Country/Region:	United States
Contact name (PI/Team):	Heather A. Carlson
Contact email (PI/Helpdesk):	carlsonh@umich.edu

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Database Commons a catalog of worldwide biological databases