Question

In homology modeling, the most suitable BLAST is

• A. PSI-BLAST
• B. PHI-BLAST
• C. Geo-BLAST
• D. Rp-BLAST

Hint:

When performing homology modeling, always prefer PSI-BLAST for more accurate and sensitive homolog detection.

Answer 1

The Correct Option is A

In homology modeling, the objective is to predict the 3D structure of a protein based on its sequence similarity to a known protein structure. To achieve this, BLAST (Basic Local Alignment Search Tool) is used to identify homologous sequences.
(1) PSI-BLAST (Position-Specific Iterative BLAST):
PSI-BLAST is the most suitable tool for homology modeling. It is an iterative version of BLAST that refines the search for homologous sequences in multiple rounds. After each round, PSI-BLAST generates a position-specific scoring matrix (PSSM), which improves the detection of distant homologs that might not be detected in a single BLAST search. This iterative process helps to improve the sensitivity and accuracy of the search, making it ideal for identifying homologous proteins that are important for structure prediction.

(2) Why Other BLAST Variants Are Less Suitable:
- PHI-BLAST: This variant is designed for detecting motifs in sequences and is not ideal for homology modeling, where the primary goal is to find overall sequence similarity.
- Geo-BLAST: Geo-BLAST focuses on genomic data and local alignments, which are not suitable for the broad sequence alignment required in homology modeling.
- Rp-BLAST: Rp-BLAST is an older version of BLAST and lacks the advanced features of PSI-BLAST, such as iterative refinement, which are crucial for detecting distant homologs in homology modeling.

Conclusion: The most suitable BLAST tool for homology modeling is PSI-BLAST, as it uses an iterative process to improve the detection of homologous sequences that are crucial for accurate structure prediction.