PDBsum

PDBsum

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PDBsum is a comprehensive database that provides detailed structural information on proteins and other macromolecules. It is a valuable resource for researchers in the field of structural biology, offering a wide range of data derived from the Protein Data Bank (PDB).

Overview

PDBsum is maintained by the European Bioinformatics Institute (EBI) and serves as a graphical overview of the contents of each PDB entry. It provides a wealth of information, including:

• Protein structure diagrams: Schematic diagrams of protein structures, showing secondary structure elements such as alpha helices and beta sheets.
• Protein-ligand interactions: Detailed views of how small molecules, such as drugs or cofactors, interact with proteins.
• Protein-protein interactions: Information on how proteins interact with each other within a complex.
• Functional annotations: Links to functional information from other databases, such as UniProt and InterPro.

Features

PDBsum offers several key features that make it an indispensable tool for researchers:

• Topology diagrams: These diagrams provide a simplified view of the protein's secondary structure, making it easier to understand the overall fold of the protein.
• Ligand binding: Detailed diagrams and data on how ligands bind to proteins, including hydrogen bonds and hydrophobic interactions.
• Protein domain architecture: Information on the domain structure of proteins, including domain boundaries and classifications.
• Enzyme reactions: For enzyme structures, PDBsum provides information on the enzyme's catalytic activity and the reactions it catalyzes.

Data Sources

PDBsum derives its data from the Protein Data Bank (PDB), which is the primary repository for 3D structural data of biological macromolecules. PDBsum processes this data to generate its detailed diagrams and annotations.

Applications

PDBsum is widely used in the fields of bioinformatics, computational biology, and drug discovery. It helps researchers understand the structural basis of protein function and interaction, which is crucial for designing new drugs and understanding disease mechanisms.

History

PDBsum was first launched in 1995 and has since become a key resource for structural biologists. It has evolved over the years to incorporate new features and data types, keeping pace with advances in structural biology.

Also see

• Protein Data Bank
• UniProt
• InterPro
• Structural biology
• Bioinformatics

External links

• PDBsum official website