Structural databases MCQs With Answer

Structural Databases MCQs With Answer is a focused quiz set designed for M.Pharm students studying Bioinformatics and Computational Biotechnology. This collection highlights the key repositories and resources used to store, retrieve, validate, and analyze three‑dimensional structures of proteins, nucleic acids, and small-molecule ligands. Questions cover primary archives (PDB), classification systems (SCOP, CATH), file formats (PDB, mmCIF), validation tools, ligand chemical component dictionaries, and modern predictive resources (AlphaFold). These MCQs emphasize applications relevant to drug discovery — e.g., binding site analysis, structural quality metrics, and homology models — helping students consolidate conceptual knowledge and practical database skills needed for structure-based drug design and interpretation of structural data.

Q1. Which database is the primary global archive of experimentally determined 3D macromolecular structures?

• RCSB Protein Data Bank (PDB)
• SCOP (Structural Classification of Proteins)
• UniProt Knowledgebase
• AlphaFold Protein Structure Database

Correct Answer: RCSB Protein Data Bank (PDB)

Q2. Which file format has become the recommended replacement for the legacy PDB format and supports richer metadata?

• PDBx/mmCIF
• FASTQ
• SDF
• CLUSTAL

Correct Answer: PDBx/mmCIF

Q3. What does a PDB “resolution” value (in Å) typically describe for X‑ray crystal structures?

• The level of detail observable in the electron density map
• The number of amino acids in the protein chain
• The computational time used to solve the structure
• The pH at which the crystal was grown

Correct Answer: The level of detail observable in the electron density map

Q4. Which resource provides a curated classification of protein domain structural relationships primarily based on manual expert curation?

• SCOP (Structural Classification of Proteins)
• CATH (Class, Architecture, Topology, Homologous superfamily)
• PDBe
• MMDB (Molecular Modeling Database)

Correct Answer: SCOP (Structural Classification of Proteins)

Q5. Which database specifically archives three‑dimensional cryo‑EM maps and associated segmentation (density) data?

• EMDB (Electron Microscopy Data Bank)
• PDB Chemical Component Dictionary
• Swiss-Model Repository
• ModBase

Correct Answer: EMDB (Electron Microscopy Data Bank)

Q6. Which PDB resource or tool provides per-structure validation reports including geometry, clashes and Ramachandran statistics?

• PDB Validation Reports (RCSB/PDBe validation pipeline)
• Pfam family pages
• KEGG Ligand Browser
• BLAST sequence alignment

Correct Answer: PDB Validation Reports (RCSB/PDBe validation pipeline)

Q7. What does RMSD (root-mean-square deviation) measure when comparing two protein structures?

• Average atomic positional difference after optimal superposition
• Sequence identity percentage between two proteins
• Difference in experimental temperature factors (B-factors)
• Variation in residue solvent accessibility

Correct Answer: Average atomic positional difference after optimal superposition

Q8. Which database stores experimentally observed small molecules and their chemical descriptions used as ligands in PDB entries?

• PDB Chemical Component Dictionary (Ligand Expo)
• DrugBank
• UniProt
• Pfam

Correct Answer: PDB Chemical Component Dictionary (Ligand Expo)

Q9. Which resource maps PDB structures to UniProt sequences and helps reconcile residue numbering between sequence and structure?

• SIFTS (Structure Integration with Function, Taxonomy and Sequences)
• PROSITE
• KEGG Orthology
• InterProScan

Correct Answer: SIFTS (Structure Integration with Function, Taxonomy and Sequences)

Q10. For NMR-derived structures deposited in the PDB, what does the archive typically store that reflects experimental ambiguity?

• An ensemble of models representing conformational variability
• A single lowest-energy minimized model only
• Only the backbone trace without side chains
• Only chemical shift tables without coordinates

Correct Answer: An ensemble of models representing conformational variability

Q11. Which database provides computed homology models for proteins lacking experimental structures?

• ModBase
• EMDB
• PDBsum
• PDBeChem

Correct Answer: ModBase

Q12. Which PDB annotation indicates the biologically relevant oligomeric state as opposed to the asymmetric unit present in the crystallographic file?

• Biological assembly (author-specified or PISA-predicted)
• Primary citation DOI
• Experimental method tag
• Sequence ORF annotation

Correct Answer: Biological assembly (author-specified or PISA-predicted)

Q13. Which tool/database is widely used to predict structures using machine learning and provides precomputed models for many proteins?

• AlphaFold Protein Structure Database
• CDD (Conserved Domain Database)
• MolProbity
• PRODRG

Correct Answer: AlphaFold Protein Structure Database

Q14. What information is contained in PDB structure factor files (or electron density maps) that is essential for validating crystallographic models?

• Observed diffraction amplitudes or intensities used to compute electron density maps
• Primary amino acid sequences only
• Predicted docking poses for ligands
• Thermodynamic binding free energies

Correct Answer: Observed diffraction amplitudes or intensities used to compute electron density maps

Q15. Which resource provides simplified schematic summaries of PDB entries including topology diagrams, ligand interactions, and domain organization?

• PDBsum
• EMDB
• AlphaFill
• ModBase

Correct Answer: PDBsum

Q16. What is the principal purpose of PDB deposition by experimentalists?

• Publicly archive coordinate data and experimental metadata to ensure reproducibility and reuse
• Provide a platform for commercial drug sales
• Replace peer review for manuscripts
• Store only raw experimental images without coordinates

Correct Answer: Publicly archive coordinate data and experimental metadata to ensure reproducibility and reuse

Q17. In the context of structure-based drug design, which PDB-derived resource helps assess likely quaternary assembly interfaces and stability?

• PISA (Protein Interfaces, Surfaces and Assemblies)
• UniProtKB function annotations
• KEGG pathway maps
• BLAST sequence hits

Correct Answer: PISA (Protein Interfaces, Surfaces and Assemblies)

Q18. Which file extension is commonly associated with the legacy plain-text coordinate format for structures?

• .pdb
• .fasta
• .sdf
• .xml

Correct Answer: .pdb

Q19. Which database or tool provides standardized restraint dictionaries for small molecules to be used during crystallographic refinement?

• cif/mmCIF dictionaries / CCP4 monomer libraries (e.g., AceDRG, eLBOW)
• UniProt accession files
• Pfam alignment profiles
• Swiss-Prot keyword list

Correct Answer: cif/mmCIF dictionaries / CCP4 monomer libraries (e.g., AceDRG, eLBOW)

Q20. Which of the following best describes the role of the RCSB PDB web portal for a pharmaceutics researcher?

• Search, visualize, and download structural data and annotations to support ligand binding analysis and structure-based drug design
• Provide clinical trial datasets and patient-level outcomes
• Host only genomic variant frequency tables
• Serve as a laboratory notebook for experimental protocols

Correct Answer: Search, visualize, and download structural data and annotations to support ligand binding analysis and structure-based drug design

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