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Updated: Aug 9, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships
Nicola D Gold1, Richard M Jackson
1Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
Journal of Chemical Information and Modeling
|March 28, 2006
Summary
A new database of protein-ligand binding sites aids drug design. This resource enables efficient searching for similar sites and supports pharmacophore model development.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Chemistry
Background:
- Structural information for protein-ligand binding sites is crucial for structure-based drug design.
- Understanding ligand interactions, cross-reactivity, and toxicity relies on binding site data.
- Existing data resources require efficient methods for similarity assessment and retrieval.
Purpose of the Study:
- To develop a comprehensive database of protein-ligand binding sites.
- To create a computational method for assessing binding site similarity.
- To facilitate data mining and structure-based applications in drug discovery.
Main Methods:
- Automated extraction of binding sites from the Protein Data Bank.
- Development of a geometric hashing algorithm for binding site similarity calculation.
- Creation of a relational database for site similarity retrieval and superposition.
- Inclusion of an all-against-all comparison of binding sites.
Main Results:
- A large, accessible database of known protein-ligand binding sites has been established.
- A robust method for calculating and comparing binding site similarity is implemented.
- The database supports efficient retrieval of similar binding sites and superposition.
- Demonstrated utility in determining site similarity and deriving receptor-based pharmacophore models.
Conclusions:
- The developed database and similarity method are valuable tools for structure-based drug design.
- This resource enhances the understanding of ligand binding and cross-reactivity.
- The database provides a foundation for data mining in structural biology and medicinal chemistry.
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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...
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