Introduction to protein informatics MCQs With Answer

Introduction to protein informatics MCQs With Answer

This quiz set is designed for M.Pharm students to strengthen core concepts in protein informatics relevant to drug discovery, formulation, and computational biology. It covers sequence and structure databases, alignment algorithms, structure prediction methods, annotation and functional inference, and applications such as docking and variant effect prediction. Questions focus on tools and principles used in real-world pharmaceutical research, including interpretation of Ramachandran plots, homology modeling, BLAST/PSI-BLAST logic, and protein–protein interaction resources. Use these MCQs to assess knowledge, prepare for exams, and identify areas for deeper study in computational approaches to proteins.

Q1. What is the primary purpose of the UniProt database in protein informatics?

• To store atomic coordinates of experimentally solved protein structures
• To provide curated protein sequence and functional annotation
• To host multiple sequence alignment tools online
• To predict protein tertiary structure de novo

Correct Answer: To provide curated protein sequence and functional annotation

Q2. Which algorithm is typically used for fast local sequence similarity searches against large sequence databases?

• Needleman–Wunsch global alignment
• BLAST (Basic Local Alignment Search Tool)
• Clustal Omega multiple alignment
• Chou–Fasman secondary structure prediction

Correct Answer: BLAST (Basic Local Alignment Search Tool)

Q3. PSI-BLAST improves sensitivity in detecting distant homologs by using which of the following approaches?

• Performing global alignments across entire sequences
• Building a position-specific scoring matrix (PSSM) from iterative hits
• Using physicochemical property clustering of amino acids
• Applying ab initio structure prediction to infer homology

Correct Answer: Building a position-specific scoring matrix (PSSM) from iterative hits

Q4. Which repository is the primary source for experimentally determined three-dimensional protein structures?

• Pfam
• UniProt
• Protein Data Bank (PDB)
• STRING

Correct Answer: Protein Data Bank (PDB)

Q5. In multiple sequence alignment, conservation of residues is most useful for identifying:

• Protein solubility properties in vitro
• Functionally or structurally important residues (active sites, binding sites)
• Exact tertiary coordinates of atoms
• Post-translational modification mass shifts

Correct Answer: Functionally or structurally important residues (active sites, binding sites)

Q6. Which method is most appropriate when a good structural template (>30% identity) is available for modeling a target protein?

• Homology (comparative) modeling
• Ab initio prediction
• Threading with no template
• Secondary structure prediction only

Correct Answer: Homology (comparative) modeling

Q7. The Ramachandran plot is primarily used to assess which aspect of a protein model?

• Sequence conservation across species
• Allowed backbone dihedral angles (phi, psi) and stereochemical quality
• Side-chain rotamer distributions only
• Hydrophobicity and solvent accessibility

Correct Answer: Allowed backbone dihedral angles (phi, psi) and stereochemical quality

Q8. Which tool or database is commonly used to identify protein families and conserved domains using HMM profiles?

• SWISS-MODEL
• Pfam
• Rosetta
• ClustalW

Correct Answer: Pfam

Q9. In docking and scoring for small-molecule binding, RMSD (root mean square deviation) between predicted and experimental ligand positions is used to evaluate:

• Thermodynamic binding free energy directly
• Geometric similarity of ligand poses to a reference structure
• Sequence alignment accuracy
• Protein backbone flexibility only

Correct Answer: Geometric similarity of ligand poses to a reference structure

Q10. Which of the following prediction methods leverages evolutionary information (multiple sequence alignments) to improve secondary structure prediction accuracy?

• Chou–Fasman
• PSIPRED
• Kyte–Doolittle hydropathy plot
• Rosetta ab initio folding

Correct Answer: PSIPRED

Q11. Hidden Markov Models (HMMs) in protein informatics are most often used for:

• Predicting three-dimensional atomic coordinates from scratch
• Modeling sequence families and detecting domain-level homology
• Calculating docking binding energies
• Direct visualization of electron density maps

Correct Answer: Modeling sequence families and detecting domain-level homology

Q12. Which resource integrates known and predicted protein–protein interactions useful for exploring pathways relevant to drug targets?

• STRING database
• EBI-PICR
• SIFT
• PROSITE

Correct Answer: STRING database

Q13. Which computational tool predicts the likely functional impact of a missense variant on protein function by considering conservation and physicochemical differences?

• SWISS-MODEL
• PolyPhen-2
• Clustal Omega
• Phyre2

Correct Answer: PolyPhen-2

Q14. Threading (fold recognition) differs from homology modeling because threading:

• Requires >90% sequence identity with template
• Aligns a query sequence to structural templates even with low sequence identity by matching fold compatibility
• Predicts protein–protein interactions directly
• Only predicts secondary structure elements

Correct Answer: Aligns a query sequence to structural templates even with low sequence identity by matching fold compatibility

Q15. Which metric is commonly used to compare two protein structures and quantify their similarity after superposition?

• Bit score
• RMSD (root mean square deviation)
• Kd (dissociation constant)
• Sequence identity percentage only

Correct Answer: RMSD (root mean square deviation)

Q16. For annotating enzymatic function from sequence, which resource provides enzyme commission numbers and curated enzyme information linked to protein entries?

• PROSITE motifs
• Enzyme nomenclature via UniProt and curated annotation (EC numbers)
• Pfam HMMs only
• ClustalW alignments

Correct Answer: Enzyme nomenclature via UniProt and curated annotation (EC numbers)

Q17. Which approach is most suitable for designing mutations to improve enzyme thermostability when a high-quality structure is available?

• Random in vitro mutagenesis with no structural guidance
• Structure-guided mutagenesis targeting surface loops, salt bridges, or packing to increase stability
• Only modifying N-terminal signal peptides
• Relying exclusively on multiple sequence alignment without structural context

Correct Answer: Structure-guided mutagenesis targeting surface loops, salt bridges, or packing to increase stability

Q18. MolProbity is a tool primarily used for:

• Predicting protein–ligand binding affinities
• Validating structural models by checking geometry, clashes, and rotamers
• Constructing multiple sequence alignments
• Calculating evolutionary rates across a phylogeny

Correct Answer: Validating structural models by checking geometry, clashes, and rotamers

Q19. Which concept explains why conserved residues in an active site are prioritized as drug design hotspots?

• Conserved residues are less likely to be functionally important
• Conserved residues indicate evolutionary constraint and are often essential for function, making them stable drug targets
• Conserved residues always confer high solubility to proteins
• Conserved residues disappear across orthologs

Correct Answer: Conserved residues indicate evolutionary constraint and are often essential for function, making them stable drug targets

Q20. Which technique combines mass spectrometry proteomics data with sequence databases to identify proteins and map post-translational modifications?

• X-ray crystallography
• Database search-based proteomics (peptide-spectrum matching) using search engines like Mascot or Sequest
• PSIPRED secondary structure prediction
• Homology modeling with SWISS-MODEL

Correct Answer: Database search-based proteomics (peptide-spectrum matching) using search engines like Mascot or Sequest

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