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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
Tiqing Liu1, Yuhmei Lin, Xin Wen
1Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
Nucleic Acids Research
|December 6, 2006
Summary
BindingDB is a database of protein-ligand binding affinities, crucial for drug discovery research. It provides experimentally determined data for over 110 protein targets and 11,000 ligands.
Area of Science:
- Biochemistry
- Pharmacology
- Structural Biology
Background:
- Protein-ligand binding affinities are critical for understanding biological processes and developing new therapeutics.
- Publicly accessible databases are essential for researchers to access and analyze binding data.
- The Protein Data Bank (PDB) and PubMed are key resources for structural and literature data.
Purpose of the Study:
- To describe the BindingDB database, a resource for experimentally determined protein-ligand binding affinities.
- To highlight the scope and content of BindingDB, including protein targets, ligands, and data sources.
- To outline the functionalities and data retrieval options offered by the BindingDB website.
Main Methods:
- Data compilation from scientific literature, focusing on drug targets with available structural data in the PDB.
- Development of a web interface supporting diverse query types (chemical structure, sequence, names, affinity, molecular weight).
- Integration of links to PDB IDs for structural data and PubMed IDs for literature references.
Main Results:
- BindingDB contains approximately 20,000 experimentally determined binding affinities for 110 protein targets and 11,000 small molecule ligands.
- The database supports advanced search functionalities, including chemical structure and similarity searches.
- Downloadable data sets (SDfiles) are available for further analysis and virtual screening.
Conclusions:
- BindingDB serves as a valuable, publicly accessible resource for researchers in drug discovery and chemical biology.
- The database facilitates the integration of binding affinity data with structural and literature information.
- BindingDB supports various applications, from data analysis to virtual screening of compound libraries.
Related Concept Videos
02:18The Equilibrium Binding Constant and Binding Strength
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
02:18The Equilibrium Binding Constant and Binding Strength
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
02:40Ligand Binding Sites
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
02:40Ligand Binding Sites
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...