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Binding MOAD specifications

Information


Unique identifier OMICS_01900
Name Binding MOAD
Alternative name Binding Mother of All Databases
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Heather A Carlson

Additional information


http://www.bindingmoad.org/Home/faq

Publications for Binding Mother of All Databases

Binding MOAD citations

 (5)
library_books

Improving the performance of the PLB index for ligand binding site prediction using dihedral angles and the solvent accessible surface area

2016
Sci Rep
PMCID: 5020399
PMID: 27619067
DOI: 10.1038/srep33232

[…] Set N: We constructed a non-redundant database, set N, consisting of 6,635 ligand-bound structures obtained from the Binding MOAD released in 2014  to derive the MF-RA. Binding MOAD groups structures at the 90% sequence identity level, and all of the structures in Binding MOAD having more than 70% sequence identity […]

library_books

Curation and Analysis of Multitargeting Agents for Polypharmacological Modeling

2014
J Chem Inf Model
PMCID: 4170814
PMID: 25133604
DOI: 10.1021/ci500092j

[…] LigandExpo (formerly known as LigandDepot), Protein Data Bank (PDB), Universal Protein Resource (UniProt), and DrugBank. A variety of ligand-protein binding databases such as PDBbind, BindingDB, and Binding MOAD are also taken into consideration in order to extract the available ligand binding affinities. Additionally, literature reports were also mined to obtain as much biological data as possib […]

library_books

AutoDock4Zn: An Improved AutoDock Force Field for Small Molecule Docking to Zinc Metalloproteins

2014
J Chem Inf Model
PMCID: 4144784
PMID: 24931227
DOI: 10.1021/ci500209e

[…] er a wide range of structure diversity and binding affinity, thus providing an optimal calibration set for generic applicability of the force field for drug design.In order to build the data set, the Binding MOAD was filtered using the following criteria: (a) presence of at least one zinc ion; (b) experimentally determined inhibition (Ki) or dissociation (Kd) constants; (c) no alternate conformati […]

library_books

Comparing Neural Network Scoring Functions and the State of the Art: Applications to Common Library Screening

2013
J Chem Inf Model
PMCID: 3735370
PMID: 23734946
DOI: 10.1021/ci400042y

[…] ested whether or not correlations exist between the molecular properties and experimentally measured binding affinities of known ligands independent of receptor. All the binding data deposited in the Binding MOAD database as of March 2013 was considered. In total, 2081 entries representing 1598 unique compounds had both known structures and precise or approximate Ki measurements (i.e., measurement […]

library_books

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

2011
J Chem Inf Model
PMCID: 3180202
PMID: 21728306
DOI: 10.1021/ci200082t

[…] ographic additives were removed. To allow users to examine the locations of additives, ions, and other copies of the ligands in multimeric structure, we included the complete, corrected biounits from Binding MOAD.Each ligand was then prepared via the Sybyl program. AM1-BCC charges assigned to the ligand were calculated via OpenEye QUACPAC() 1.3.1. File conversion and postprocessing was performed t […]

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Binding MOAD institution(s)
Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
Binding MOAD funding source(s)
Supported by National Science Foundation [MCB 0546073]; National Institutes of Health [U01 GM086873]; National Center for Advancing Translational Sciences (NCATS) [UL1TR000433].

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