Q.19 An example of a derived protein structure database is
(A) Pfam (B) SCOP (C) GEO (D) Prosite
Derived protein structure databases process primary experimental data (PDB coordinates) into hierarchical classifications revealing evolutionary relationships among 3D folds. Unlike sequence-only or primary structure repositories, these databases group proteins by structural similarity independent of sequence conservation. SCOP exemplifies this approach for biotechnology applications in fold prediction and drug design.
Correct Answer
SCOP (B) qualifies as the derived protein structure database. It manually curates Protein Data Bank (PDB) structures into a hierarchy: Class → Fold → Superfamily → Family → Protein → Species → Structure, capturing remote homologs sharing <20% sequence identity but conserved core topology. This structural phylogeny proves essential for function prediction when sequence homology fails.
Option Explanations
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Pfam (A): Protein family database of sequence alignments and HMM profiles; classifies by primary sequence motifs, not 3D structure
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SCOP (B): Derived structure database—hierarchically classifies PDB coordinates by fold topology, detecting evolutionary relationships invisible to sequence methods
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GEO (C): Gene Expression Omnibus stores microarray/RNA-seq functional genomics data; no protein structure content whatsoever
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Prosite (D): Sequence pattern/motif database for functional sites (e.g., phosphorylation, active sites); lacks 3D structural classification
Bioinformatics Applications
SCOP hierarchies guide protein engineering in Jaipur biotech labs, identifying catalytically active scaffolds for enzyme redesign during microbial fermentation optimization. Integration with AlphaFold predicted structures expands coverage 1000-fold, enhancing SEO-optimized publications on structural bioinformatics and molecular modeling workflows.
