Applications of bioinformatics MCQs With Answer

Applications of bioinformatics MCQs With Answer

This quiz collection is tailored for M.Pharm students to deepen understanding of practical bioinformatics applications in pharmaceutical research. It covers sequence analysis, structural bioinformatics, cheminformatics, pharmacogenomics, omics data interpretation, virtual screening and ADMET prediction — areas frequently encountered in drug discovery and development. Each question is crafted to test conceptual knowledge and real-world application, emphasizing methods, databases and analytical approaches used for target identification, lead optimization, biomarker discovery and personalized medicine. Use these MCQs to assess readiness for research tasks, viva voce and semester exams while reinforcing how computational tools integrate with experimental pharmacology.

Q1. Which primary function of the BLAST tool is most directly useful in drug target identification?

• Predict three‑dimensional structure of proteins
• Identify homologous sequences and potential conserved functional residues
• Simulate ligand‑binding dynamics
• Predict ADMET properties of small molecules

Correct Answer: Identify homologous sequences and potential conserved functional residues

Q2. Which public database is the standard resource for experimentally determined protein 3D structures used in structure‑based drug design?

• GenBank
• PDB (Protein Data Bank)
• KEGG
• ArrayExpress

Correct Answer: PDB (Protein Data Bank)

Q3. Molecular docking primarily predicts which of the following for a ligand‑target pair?

• Changes in gene expression after ligand binding
• Preferred orientation and an estimate of binding affinity of a ligand to a target
• Protein secondary structure from sequence
• Metabolic stability in hepatocytes

Correct Answer: Preferred orientation and an estimate of binding affinity of a ligand to a target

Q4. What is the core concept behind QSAR (Quantitative Structure–Activity Relationship) modeling in drug discovery?

• Relating chemical structure descriptors with observed biological activity to predict potency
• Predicting protein tertiary structure from sequence
• Mapping metabolic pathways in microbes
• Aligning genomic sequences across species

Correct Answer: Relating chemical structure descriptors with observed biological activity to predict potency

Q5. How does pharmacogenomics application of bioinformatics improve patient therapy?

• By predicting solubility of oral formulations
• By selecting drug dose or therapy based on individual genetic variants affecting drug response
• By designing better analytical methods for drug assays
• By forecasting market demand for a drug

Correct Answer: By selecting drug dose or therapy based on individual genetic variants affecting drug response

Q6. What is the role of in silico ADMET prediction tools during lead optimization?

• Calculating Gibbs free energy of protein folding
• Predicting absorption, distribution, metabolism, excretion and toxicity properties to prioritize compounds
• Generating synthetic routes for scale‑up
• Designing primers for PCR

Correct Answer: Predicting absorption, distribution, metabolism, excretion and toxicity properties to prioritize compounds

Q7. Homology (comparative) modeling of a protein structure relies primarily on which assumption?

• Proteins with similar isoelectric points have identical folds
• Proteins with significant sequence homology adopt similar three‑dimensional structures
• All membrane proteins form alpha‑helical bundles
• Ligand binding sites are always located in conserved domains

Correct Answer: Proteins with significant sequence homology adopt similar three‑dimensional structures

Q8. Which high‑throughput technique combined with bioinformatics is most suitable for discovering expression‑based biomarkers in disease?

• Chromatography coupled to mass spectrometry for small molecules
• RNA‑Seq followed by differential expression and pathway analysis
• Surface plasmon resonance for binding kinetics
• X‑ray crystallography of proteins

Correct Answer: RNA‑Seq followed by differential expression and pathway analysis

Q9. For identifying differentially expressed genes between treated and control samples, which bioinformatics approach is most appropriate?

• Genome assembly
• RNA‑Seq analysis using normalization and statistical testing
• Homology modeling of enzymes
• Ligand‑based pharmacophore generation

Correct Answer: RNA‑Seq analysis using normalization and statistical testing

Q10. Network pharmacology is primarily used to study which aspect of drug action?

• Single enzyme kinetics in isolation
• Interactions among multiple targets, pathways and drugs to explain polypharmacology
• Physicochemical solubility enhancement techniques
• Quality control of manufactured tablets

Correct Answer: Interactions among multiple targets, pathways and drugs to explain polypharmacology

Q11. Molecular dynamics (MD) simulations are best suited to investigate which property of a drug‑target complex?

• Long‑term population pharmacokinetics in humans
• Atomic‑level conformational flexibility and stability over time
• Primary sequence mutations in genes
• Solubility in different pH media

Correct Answer: Atomic‑level conformational flexibility and stability over time

Q12. If the target structure is unknown, which virtual screening strategy is typically applied?

• Structure‑based docking against the target binding pocket
• Pharmacophore modeling and similarity‑based ligand screening
• MD simulations of the apo protein structure
• Ramachandran plot analysis

Correct Answer: Pharmacophore modeling and similarity‑based ligand screening

Q13. Bioinformatics prediction of CRISPR‑Cas9 off‑target sites relies mainly on which factor?

• Metabolic stability of the guide RNA
• Sequence similarity and PAM context across the genome to identify potential off‑targets
• Protein tertiary structure of Cas9
• Molecular weight of guide RNA

Correct Answer: Sequence similarity and PAM context across the genome to identify potential off‑targets

Q14. Which database would you consult for curated small‑molecule bioactivity and target information useful in lead discovery?

• Pfam
• ChEMBL
• UniProtKB/Swiss‑Prot
• ENA (European Nucleotide Archive)

Correct Answer: ChEMBL

Q15. Pathway enrichment analysis of differentially expressed genes helps a pharmaceutical researcher to:

• Predict three‑dimensional structures of all proteins encoded by those genes
• Identify biological pathways significantly affected by treatment or disease, suggesting mechanisms or targets
• Directly measure drug concentrations in plasma samples
• Design clinical trial randomization schemes

Correct Answer: Identify biological pathways significantly affected by treatment or disease, suggesting mechanisms or targets

Q16. Tools like HMMER and Pfam are primarily used in bioinformatics to:

• Predict small‑molecule ADMET profiles
• Detect conserved protein domains and families using hidden Markov models
• Estimate drug market size
• Simulate ligand binding free energy directly

Correct Answer: Detect conserved protein domains and families using hidden Markov models

Q17. In virtual screening validation, which metric specifically evaluates early recognition of actives in a ranked library?

• Root mean square deviation (RMSD)
• Enrichment Factor (EF)
• pKa value
• Retention time in HPLC

Correct Answer: Enrichment Factor (EF)

Q18. Which algorithm/tool is widely used for multiple sequence alignment relevant for phylogenetics and conserved motif detection?

• Clustal Omega
• AutoDock Vina
• GROMACS
• SwissADME

Correct Answer: Clustal Omega

Q19. De novo peptide sequencing from tandem mass spectrometry data is mainly applied to:

• Predict small‑molecule solubility
• Infer peptide amino‑acid sequences directly from MS/MS spectra without a database
• Design PCR primers for gene cloning
• Model membrane permeability of drugs

Correct Answer: Infer peptide amino‑acid sequences directly from MS/MS spectra without a database

Q20. A Ramachandran plot in structural bioinformatics is used to:

• Assess the stereochemical quality of a protein model by showing allowed backbone dihedral angles
• Compute ligand binding free energy
• Predict mRNA secondary structure
• Measure compound lipophilicity (LogP)

Correct Answer: Assess the stereochemical quality of a protein model by showing allowed backbone dihedral angles

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