Chemoinformatics and its applications MCQs With Answer

Chemoinformatics integrates chemistry, informatics and computational tools to manage and analyze chemical data for drug discovery and pharmaceutical research. Key concepts include molecular descriptors, fingerprints, QSAR, virtual screening, ADMET prediction and database mining using formats like SMILES, InChI and SDF. Practical tools and platforms (RDKit, OpenBabel, PubChem, KNIME) enable similarity searching, docking, pharmacophore modeling and machine‑learning driven lead optimization. Understanding data curation, descriptor selection, validation methods and drug‑likeness filters (Lipinski, PAINS) is essential for B.Pharm students applying chemoinformatics to formulation, lead identification and safety assessment. Now let’s test your knowledge with 30 MCQs on this topic.

Q1. What is the primary goal of chemoinformatics in pharmaceutical research?

• To synthesize new chemical compounds in the lab
• To store physical samples in chemical libraries
• To manage and analyze chemical data for drug discovery and decision making
• To exclusively perform clinical trials

Correct Answer: To manage and analyze chemical data for drug discovery and decision making

Q2. Which line notation is commonly used to represent chemical structures as ASCII strings?

• FASTA
• SMILES
• HTML
• JPEG

Correct Answer: SMILES

Q3. What does InChI primarily provide for chemical structures?

• A generic image of the molecule
• A standardized textual identifier encoding connectivity and stereochemistry
• A 3D coordinate file for molecular dynamics
• A calculated logP value

Correct Answer: A standardized textual identifier encoding connectivity and stereochemistry

Q4. Which file format commonly stores multiple molecules along with associated properties?

• SDF (Structure-Data File)
• TXT
• CSV
• PNG

Correct Answer: SDF (Structure-Data File)

Q5. What is a molecular descriptor?

• A laboratory protocol for synthesis
• A numeric or categorical value summarizing molecular properties or structure
• A type of clinical endpoint
• A visual rendering of a protein

Correct Answer: A numeric or categorical value summarizing molecular properties or structure

Q6. How do 2D descriptors differ from 3D descriptors?

• 2D descriptors require quantum calculations, 3D descriptors do not
• 2D descriptors use connectivity and topology; 3D descriptors depend on molecular conformation and spatial coordinates
• 3D descriptors are always faster to compute than 2D
• 2D descriptors represent protein targets, 3D represent ligands

Correct Answer: 2D descriptors use connectivity and topology; 3D descriptors depend on molecular conformation and spatial coordinates

Q7. What are chemical fingerprints used for?

• Encoding chromatographic retention times
• Representing molecular features as bit vectors for similarity searching and clustering
• Animating molecular videos
• Measuring experimental purity

Correct Answer: Representing molecular features as bit vectors for similarity searching and clustering

Q8. Which similarity metric is most commonly used with binary fingerprints?

• Euclidean distance
• Tanimoto coefficient
• Pearson correlation
• Manhattan distance

Correct Answer: Tanimoto coefficient

Q9. What is the Extended-Connectivity Fingerprint (ECFP) also known as?

• Morgan fingerprint
• Smith fingerprint
• HPLC fingerprint
• Gaussian fingerprint

Correct Answer: Morgan fingerprint

Q10. What is MACCS in chemoinformatics?

• A set of 166 predefined structural keys used as fingerprints
• A molecular dynamics engine
• An NMR technique
• A clinical trial phase

Correct Answer: A set of 166 predefined structural keys used as fingerprints

Q11. What does QSAR modeling aim to predict?

• The most stable crystal habit
• Quantitative relationship between chemical structure and biological or physicochemical activity
• Patent expiration dates
• The manufacturing yield in synthesis

Correct Answer: Quantitative relationship between chemical structure and biological or physicochemical activity

Q12. What is a pharmacophore model?

• A full 3D atomic model of a protein-ligand complex
• An abstract representation of essential steric and electronic features required for biological activity
• A type of mass spectrometry output
• A chemical safety data sheet

Correct Answer: An abstract representation of essential steric and electronic features required for biological activity

Q13. What is virtual screening?

• Screening compounds using only wet-lab bioassays
• In silico evaluation of large chemical libraries to identify potential actives
• A method to visualize chemical reactions
• Testing drug formulations for stability

Correct Answer: In silico evaluation of large chemical libraries to identify potential actives

Q14. What is the primary objective of molecular docking in drug discovery?

• Predicting synthetic routes
• Estimating the binding pose and relative affinity between ligand and target
• Measuring solubility experimentally
• Designing clinical trial protocols

Correct Answer: Estimating the binding pose and relative affinity between ligand and target

Q15. ADMET prediction in chemoinformatics refers to forecasting what?

• Analytical methods for chromatography
• Absorption, Distribution, Metabolism, Excretion and Toxicity properties
• Atomic numbers and electron counts
• Regulatory submission timelines

Correct Answer: Absorption, Distribution, Metabolism, Excretion and Toxicity properties

Q16. Which rule addresses oral bioavailability and is often used as a drug-likeness filter?

• Beer’s Law
• Lipinski’s Rule of Five
• Le Chatelier’s Principle
• Henderson-Hasselbalch equation

Correct Answer: Lipinski’s Rule of Five

Q17. What is scaffold hopping in ligand design?

• Switching the route of synthesis
• Finding different core frameworks that retain biological activity
• Moving compounds between physical storage shelves
• Changing assay types from enzymatic to cellular

Correct Answer: Finding different core frameworks that retain biological activity

Q18. Why use ensemble docking instead of a single receptor conformation?

• To reduce computational cost
• To sample multiple receptor conformations and capture bindingsite flexibility
• To avoid using 3D structures entirely
• To only screen peptides

Correct Answer: To sample multiple receptor conformations and capture bindingsite flexibility

Q19. What is the purpose of conformer generation in 3D chemoinformatics workflows?

• To build proteomics databases
• To enumerate plausible 3D geometries of a molecule for docking or descriptor calculation
• To calculate pH of solutions
• To sequence DNA

Correct Answer: To enumerate plausible 3D geometries of a molecule for docking or descriptor calculation

Q20. What is k-fold cross-validation used for in QSAR modeling?

• Partitioning data to assess model generalizability and avoid overfitting
• Measuring physical purity of a sample
• Optimizing chemical synthesis yields
• Visualizing molecular orbitals

Correct Answer: Partitioning data to assess model generalizability and avoid overfitting

Q21. What does overfitting mean in machine learning models for chemoinformatics?

• Model performs well on new external data but poorly on training data
• Model fits noise in the training data and performs poorly on unseen data
• Model is too simple and underestimates activities
• Model uses too few descriptors intentionally

Correct Answer: Model fits noise in the training data and performs poorly on unseen data

Q22. What does ROC-AUC measure in classification tasks?

• The molecular weight distribution in a dataset
• The ability of a classifier to discriminate between classes across thresholds
• The average logP value of actives
• The number of descriptors used

Correct Answer: The ability of a classifier to discriminate between classes across thresholds

Q23. Why is descriptor scaling important before many machine-learning algorithms?

• It makes chemical synthesis easier
• To ensure features contribute proportionally and avoid dominance by large-scale descriptors
• It increases the number of descriptors automatically
• It converts SMILES to InChI

Correct Answer: To ensure features contribute proportionally and avoid dominance by large-scale descriptors

Q24. What does canonicalization of SMILES achieve?

• Converts molecules into 3D coordinates
• Produces a unique SMILES string for a given molecular structure
• Annotates spectra with peaks
• Determines pKa values

Correct Answer: Produces a unique SMILES string for a given molecular structure

Q25. Which public database is widely used for chemical structures and bioactivity data?

• PubChem
• ClinicalTrials.gov only
• Wikipedia Chemistry
• Google Maps

Correct Answer: PubChem

Q26. Which open-source toolkit is commonly used for cheminformatics tasks like fingerprinting and file conversion?

• Photoshop
• RDKit
• Excel only
• SPSS

Correct Answer: RDKit

Q27. What is Principal Component Analysis (PCA) used for in chemoinformatics?

• Predicting reaction kinetics
• Reducing dimensionality to visualize and interpret descriptor space
• Generating SMILES strings
• Measuring assay signal intensity

Correct Answer: Reducing dimensionality to visualize and interpret descriptor space

Q28. What is the purpose of clustering compounds in chemical space?

• To randomize assay plates
• To group structurally similar compounds for diversity analysis and library design
• To perform mass spectrometry
• To increase molecular weight

Correct Answer: To group structurally similar compounds for diversity analysis and library design

Q29. What are PAINS filters used for in virtual screening?

• Predicting oral absorption rates
• Identifying substructures that commonly give false positives in bioassays
• Optimizing synthetic yields
• Annotating NMR spectra

Correct Answer: Identifying substructures that commonly give false positives in bioassays

Q30. Why is data curation essential before building chemoinformatics models?

• It is optional and rarely affects results
• To remove duplicates, correct errors, standardize structures and improve model reliability
• To convert all molecules to proteins
• To automatically synthesize compounds

Correct Answer: To remove duplicates, correct errors, standardize structures and improve model reliability

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