Predicting Functional Regions in the Protein Sequence using SMART

Prediction of functional regions in the protein sequence plays a crucial role in the computer-aided drug discovery. SMART (a Simple Modular Architecture Research Tool) helps identify and annotate protein domains and analyze domain architectures by BLAST search.

In bioinformatics, domains refer to distinct functional, structural, or evolutionary units within proteins, DNA, or RNA. Here are some key types of domains in bioinformatics:

1. Protein Domains

• Structural Domains: Compact, independently folding units within a protein (e.g., SH3, zinc finger, immunoglobulin domains).
• Functional Domains: Regions responsible for specific biochemical activities (e.g., kinase domain, DNA-binding domain).
• Evolutionary Domains: Conserved regions indicating common ancestry (e.g., Pfam domains).

2. DNA/RNA Domains

• Regulatory Domains: DNA regions controlling gene expression (e.g., promoters, enhancers).
• Functional RNA Domains: Motifs in non-coding RNAs (e.g., ribozyme catalytic core, miRNA seed region).

3. Computational & Database Domains

• Domain Prediction Tools:
  • Pfam (protein families)
  • InterPro (integrates multiple databases)
  • SMART (domain architectures)
  • CDD (Conserved Domain Database)
• Domain Annotation: Identifying domains in sequences for functional inference.

4. Applications

• Protein Function Prediction (domains often correlate with function).
• Drug Discovery (targeting specific domains, e.g., kinase inhibitors).
• Evolutionary Studies (domain shuffling, gene fusion events).

This a short video tutorial to identify functional domains in nucleotide binding proteins using a domain analysis server like SMART (Simple Modular Architecture Research Tool), you can upload your protein sequence and analyze the results to pinpoint regions with conserved motifs and functional significance, including nucleotide binding domains.