Protein Databases

 

Protein Databases

 

Protein databases are essential repositories of information about protein sequences, structures, and functions. These databases help researchers in zoology and related fields study the molecular biology of organisms, offering insights into protein functions, evolutionary relationships, and biochemical properties.

 

1. PIR (Protein Information Resource)

 

The Protein Information Resource (PIR) is one of the oldest protein databases, established in 1984. It is maintained by the National Biomedical Research Foundation (NBRF) and provides protein sequence data and functional annotations.

 

PIR contains protein sequences from diverse species, including animals, plants, bacteria, and viruses, with detailed annotations.

 

Features of Protein Database:

 

1)    Functional and structural annotations.

2)    Provides protein families and domain classifications.

3)    Integrates tools for protein sequence analysis and prediction.

 

 2. SWISS-PROT

 

SWISS-PROT is a manually curated protein sequence database, maintained by the Swiss Institute of Bioinformatics (SIB) and the European Bioinformatics Institute (EBI). It is known for its high level of annotation and accuracy.

 

 SWISS-PROT provides highly reliable, non-redundant protein sequence data with detailed functional information and biological significance.

 

Features of SWISS-PROT:

 

1)    Detailed annotations on protein functions, domains, post-translational modifications, and cross-references to other databases.

2)    Minimal redundancy and focus on quality over quantity.

3)    Regular updates to ensure accurate and up-to-date information.

We can explore SWISS-PROT from UniProtKB/Swiss-Prot - SIB Swiss Institute of Bioinformatics | Expasy

 3.TrEMBL (Translated EMBL)

 TrEMBL is a supplement to SWISS-PROT and contains protein sequences that are automatically annotated and not yet manually curated. It is part of the UniProt Knowledgebase (UniProtKB).

 

TrEMBL contains all protein sequences that are translated from nucleotide sequences in the EMBL database, but are yet to be reviewed and included in SWISS-PROT.

 Features of TrEMBL: 

1)    Large collection of protein sequences, including predicted proteins.

2)    Automatic functional annotations based on sequence similarity.

3)    Complements SWISS-PROT by offering a broader range of sequences.

We can explore TrEMBL from https://www.uniprot.org

 

4. PDB (Protein Data Bank)

 

The Protein Data Bank (PDB) is a global repository for the 3D structures of biological macromolecules, including proteins and nucleic acids. It is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB).

   

PDB contains experimentally determined 3D structures of proteins, DNA, RNA, and complexes, primarily from X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy.

 

Features of PDB:

1)    Provides 3D structural data of proteins and other biomolecules.

2)    Tools for visualizing, analyzing, and comparing protein structures.

3)    Links to related sequence databases and functional annotations.

We can explore PDB from www.rcsb.org

 

Protein databases like PIR, SWISS-PROT, TrEMBL, and PDB are vital tools for Computational biology. These databases allow access to a wealth of information on protein sequences, structures, and functions. These resources help to explore various aspects of molecular biology, evolutionary studies, and functional genomics across different animal species.

 

Nucleic Acid Databases , Biological Databases , Primary, Secondary and Composite Databases, Nucleic Acid Databases, Protein Databases