Q.1 What does the term "protein folding" refer to?
The process of synthesizing proteins
The arrangement of amino acids in a linear chain
The three‑dimensional arrangement of a polypeptide chain
The breakdown of proteins into amino acids
Explanation - Protein folding is the process by which a linear polypeptide chain adopts a specific 3D structure that determines its function.
Correct answer is: The three‑dimensional arrangement of a polypeptide chain
Q.2 Which of the following best describes a ligand?
A protein that binds to DNA
A molecule that binds to a target protein
An enzyme that catalyzes reactions
A cell membrane component
Explanation - In drug design, a ligand is typically a small molecule that binds to a specific site on a protein target to modulate its activity.
Correct answer is: A molecule that binds to a target protein
Q.3 Which software is commonly used for molecular docking?
MATLAB
AutoDock Vina
AutoCAD
Microsoft Excel
Explanation - AutoDock Vina is a popular, open‑source program for predicting how small molecules bind to a protein target.
Correct answer is: AutoDock Vina
Q.4 What is the primary purpose of a force field in molecular simulations?
To store protein sequences
To calculate the electronic charge distribution
To approximate inter‑atomic potentials
To visualize 3D structures
Explanation - A force field provides mathematical functions and parameters that describe the potential energy of a system, enabling simulations of molecular dynamics.
Correct answer is: To approximate inter‑atomic potentials
Q.5 In QSAR studies, which descriptor measures the overall shape of a molecule?
LogP
Molecular weight
Polar surface area
Skeletal topological index
Explanation - Skeletal topological indices quantify aspects of a molecule's shape and connectivity, useful in quantitative structure‑activity relationships.
Correct answer is: Skeletal topological index
Q.6 What is the main advantage of using a 3D pharmacophore model?
It predicts the exact binding affinity of a ligand
It identifies the most probable binding pose
It captures spatial arrangement of key features
It generates the protein's amino acid sequence
Explanation - A 3D pharmacophore model describes the spatial arrangement of features (hydrogen bond donors/acceptors, hydrophobic groups) necessary for activity.
Correct answer is: It captures spatial arrangement of key features
Q.7 Which algorithm is commonly employed to solve the protein–protein docking problem?
Monte Carlo simulated annealing
Branch‑and‑bound
Genetic algorithms
Fast Fourier Transform (FFT)
Explanation - FFT-based docking rapidly evaluates many relative orientations of two proteins by transforming shape complementarity into the frequency domain.
Correct answer is: Fast Fourier Transform (FFT)
Q.8 Which of the following best describes a homology model?
A model built from the crystal structure of the target protein
A model built using the sequence of the target protein only
A model built by aligning the target sequence to a template of known structure
A model built by random coil simulation
Explanation - Homology modeling uses a known structure of a related protein (template) to predict the structure of a protein with unknown structure.
Correct answer is: A model built by aligning the target sequence to a template of known structure
Q.9 What is the role of a water model in molecular dynamics simulations?
To define the dielectric constant of the solvent
To specify the geometry and interaction parameters of water molecules
To calculate the pKa of titratable groups
To provide a visual representation of solvent
Explanation - Water models (e.g., TIP3P, SPC/E) provide fixed positions of atoms and parameters for hydrogen bonding and electrostatics in MD simulations.
Correct answer is: To specify the geometry and interaction parameters of water molecules
Q.10 Which of these is NOT a common type of similarity search in ligand‑based drug discovery?
Tanimoto coefficient
Dice similarity
Euclidean distance
Cosine similarity
Explanation - Euclidean distance is a metric, not a similarity coefficient commonly used for chemical fingerprints; similarity indices like Tanimoto are preferred.
Correct answer is: Euclidean distance
Q.11 What does the term "binding free energy" represent in molecular docking?
The energy required to unfold a protein
The energy difference between the bound and unbound states
The kinetic barrier to ligand binding
The total potential energy of the system
Explanation - Binding free energy quantifies the thermodynamic favorability of a ligand binding to a target; lower values indicate stronger binding.
Correct answer is: The energy difference between the bound and unbound states
Q.12 Which of the following databases provides experimentally determined protein structures?
PubChem
ChEMBL
Protein Data Bank (PDB)
DrugBank
Explanation - The PDB contains 3D coordinates of proteins and nucleic acids obtained from X‑ray crystallography, NMR, and cryo‑EM.
Correct answer is: Protein Data Bank (PDB)
Q.13 In molecular dynamics, what does the term "time step" refer to?
The total simulation time
The interval at which forces are recalculated
The duration of each integration step
The time needed to equilibrate the system
Explanation - The time step is a small increment (typically 1–2 fs) used to advance the simulation via numerical integration of Newton's equations.
Correct answer is: The duration of each integration step
Q.14 Which technique is used to refine a homology model by adjusting side‑chain orientations?
Energy minimization
Loop modeling
Side‑chain packing
Molecular docking
Explanation - Side‑chain packing algorithms place side‑chains in energetically favorable conformations to improve the accuracy of a homology model.
Correct answer is: Side‑chain packing
Q.15 What is the main purpose of a pharmacophore hypothesis?
To predict the 3D structure of a protein
To guide the synthesis of new ligands
To model solvent effects in binding
To calculate binding affinities directly
Explanation - A pharmacophore hypothesis identifies key chemical features required for activity, helping chemists design molecules that satisfy those constraints.
Correct answer is: To guide the synthesis of new ligands
Q.16 Which of the following is a major limitation of docking simulations?
They require no experimental data
They perfectly predict binding poses
They neglect protein flexibility
They always use quantum mechanical calculations
Explanation - Docking often treats the protein as rigid; however, protein flexibility can significantly influence binding modes and affinities.
Correct answer is: They neglect protein flexibility
Q.17 In the context of drug discovery, what does ADMET stand for?
Absorption, Distribution, Metabolism, Excretion, Toxicity
Activity, Diffusion, Metabolism, Enzyme, Thermodynamics
Affinity, Diffusion, Metabolic, Enzyme, Tolerance
Absorption, Distribution, Metabolism, Enzyme, Transport
Explanation - ADMET describes the pharmacokinetic properties of a drug that influence its efficacy and safety profile.
Correct answer is: Absorption, Distribution, Metabolism, Excretion, Toxicity
Q.18 Which type of ligand‑based approach uses a set of known active compounds to predict new actives?
Structure‑based design
Similarity searching
Pharmacophore modeling
Molecular docking
Explanation - Similarity searching compares chemical fingerprints of known actives to find structurally similar compounds likely to be active.
Correct answer is: Similarity searching
Q.19 What does the Root‑Mean‑Square Deviation (RMSD) measure in protein‑ligand docking?
The difference in binding free energy between poses
The average distance between corresponding atoms of two conformations
The time required for a ligand to bind
The difference in solvent accessible surface area
Explanation - RMSD quantifies the structural similarity between two conformations; lower RMSD indicates more similar binding poses.
Correct answer is: The average distance between corresponding atoms of two conformations
Q.20 Which computational method is best suited to calculate accurate binding free energies including entropic contributions?
Molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA)
Docking with AutoDock Vina
Pharmacophore modeling
Ligand‑based QSAR
Explanation - MM/PBSA estimates binding free energies by combining molecular mechanics energies with solvation and entropic terms, offering higher accuracy.
Correct answer is: Molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA)
Q.21 Which of these descriptors is used to quantify lipophilicity?
LogP
Molecular weight
Number of rotatable bonds
Polar surface area
Explanation - LogP measures the partition coefficient between octanol and water, reflecting a compound's lipophilicity.
Correct answer is: LogP
Q.22 What is the primary function of the Protein–Ligand Interaction Profiler (PLIP) tool?
To generate 3D structures from sequences
To visualize protein–ligand complexes in the browser
To identify key interactions in a protein–ligand complex
To perform molecular dynamics simulations
Explanation - PLIP automatically detects hydrogen bonds, hydrophobic contacts, π‑π stacking, and salt bridges in protein–ligand complexes.
Correct answer is: To identify key interactions in a protein–ligand complex
Q.23 In virtual screening, what is the main advantage of a ‘pharmacophore‑driven’ approach?
It requires no knowledge of the target protein
It can be applied to very large chemical libraries efficiently
It predicts the exact binding free energy
It eliminates the need for experimental validation
Explanation - Pharmacophore filtering rapidly screens millions of compounds by matching key features, making it computationally inexpensive.
Correct answer is: It can be applied to very large chemical libraries efficiently
Q.24 Which of the following best describes a 'lead optimization' step?
Designing the first screening library
Improving potency, selectivity, and ADMET of a lead compound
Predicting the protein’s tertiary structure
Synthesizing a new class of drugs from scratch
Explanation - Lead optimization refines a promising hit to enhance its pharmacological profile before preclinical development.
Correct answer is: Improving potency, selectivity, and ADMET of a lead compound
Q.25 What does the term 'binding site pocket depth' refer to?
The number of hydrogen bonds in the pocket
The volume of the binding site
The distance from the surface to the deepest point of the pocket
The electrostatic potential of the pocket
Explanation - Pocket depth describes how recessed the binding cavity is, influencing ligand fit and binding mode.
Correct answer is: The distance from the surface to the deepest point of the pocket
Q.26 Which of the following is a common metric used to evaluate the quality of a docking pose?
Binding free energy
Root‑Mean‑Square Deviation (RMSD)
Molecular weight
Number of rotatable bonds
Explanation - RMSD compares the predicted pose to a reference, such as the experimentally determined pose, to gauge accuracy.
Correct answer is: Root‑Mean‑Square Deviation (RMSD)
Q.27 What is the purpose of 'solvent mapping' in ligand design?
To identify favorable binding regions for ligands
To calculate the dielectric constant of the solvent
To optimize the crystal packing of the protein
To determine the pKa of titratable residues
Explanation - Solvent mapping places probe molecules across the protein surface to reveal energetically favorable regions for ligand binding.
Correct answer is: To identify favorable binding regions for ligands
Q.28 Which of the following is NOT a typical component of a pharmacophore model?
Hydrogen bond donors
Hydrophobic centers
Rotatable bonds
Aromatic rings
Explanation - Pharmacophores focus on spatial arrangements of functional groups; rotatable bonds are not explicit features of the model.
Correct answer is: Rotatable bonds
Q.29 Which technique can be used to generate a conformational ensemble of a flexible ligand?
Molecular docking
Conformer generation algorithms
Protein‑protein docking
Sequence alignment
Explanation - Conformer generators sample the ligand's torsional space to produce multiple low‑energy structures for further screening.
Correct answer is: Conformer generation algorithms
Q.30 In a 2D chemical fingerprint, what does a 'bit' typically represent?
The presence or absence of a specific substructure
The exact 3D position of an atom
The mass of the molecule
The charge state of the molecule
Explanation - Fingerprints encode substructure presence as binary bits, facilitating rapid similarity calculations.
Correct answer is: The presence or absence of a specific substructure
Q.31 What is the main goal of 'virtual screening' in drug discovery?
To physically test all possible compounds
To identify potential active compounds computationally
To synthesize new drug candidates
To analyze pharmacokinetics experimentally
Explanation - Virtual screening uses computational methods to filter large libraries, prioritizing candidates for experimental testing.
Correct answer is: To identify potential active compounds computationally
Q.32 Which of the following best describes the 'ligand‑centric' approach in drug design?
Focus on the properties of the target protein only
Design new ligands based on known active molecules
Predict the protein structure from ligand binding
Use only physical chemistry principles
Explanation - Ligand‑centric methods such as similarity search or pharmacophore modeling rely on known actives to guide design.
Correct answer is: Design new ligands based on known active molecules
Q.33 Which computational method uses quantum mechanics to describe interactions between a ligand and a protein?
Molecular mechanics
Molecular dynamics
Quantum mechanics/molecular mechanics (QM/MM)
Pharmacophore modeling
Explanation - QM/MM treats the binding site with quantum mechanics while the rest of the system is described by molecular mechanics, allowing accurate interaction modeling.
Correct answer is: Quantum mechanics/molecular mechanics (QM/MM)
Q.34 What does a 'scaffold' refer to in medicinal chemistry?
The central core structure of a molecule
The solvent used for drug formulation
The binding site of a target protein
The computational model of a ligand
Explanation - The scaffold is the core framework upon which functional groups are added to modify activity and properties.
Correct answer is: The central core structure of a molecule
Q.35 Which of the following is a key advantage of using a coarse‑grained model in molecular simulation?
Higher accuracy of atomic details
Reduced computational cost
Exact calculation of quantum effects
Better representation of electronic structure
Explanation - Coarse‑grained models simplify systems by grouping atoms, enabling longer time‑scale simulations at lower computational expense.
Correct answer is: Reduced computational cost
Q.36 In the context of drug design, what does 'bioisostere' mean?
A compound that is biologically inactive
A group that can replace another while retaining similar biological properties
A chemical bond that is broken during metabolism
A synthetic pathway for drug production
Explanation - Bioisosteric replacement swaps functional groups to improve drug properties without changing activity.
Correct answer is: A group that can replace another while retaining similar biological properties
Q.37 Which method is commonly used to estimate the entropy change upon ligand binding?
Normal mode analysis
Docking score
Tanimoto coefficient
Sequence alignment
Explanation - Normal mode analysis approximates the vibrational entropy of a system, which contributes to binding thermodynamics.
Correct answer is: Normal mode analysis
Q.38 What is the significance of the 'pocket volume' in docking studies?
It determines the number of hydrogen bonds formed
It indicates how many ligands can fit simultaneously
It provides a measure of binding site size for ligand accommodation
It is unrelated to docking
Explanation - Pocket volume helps predict which ligands can physically occupy the site and is used in filtering steps.
Correct answer is: It provides a measure of binding site size for ligand accommodation
Q.39 Which of these is a descriptor used for modeling hydrogen bond donor ability?
HBD count
Molecular weight
LogS
Rotatable bonds
Explanation - The HBD count represents the number of hydrogen bond donors in a molecule, a key descriptor in QSAR models.
Correct answer is: HBD count
Q.40 In a molecular docking workflow, which step is performed after generating the protein–ligand complex?
Ligand synthesis
Binding free energy calculation
Protein sequence alignment
Molecular dynamics simulation
Explanation - After docking, the predicted pose is evaluated by estimating its binding free energy to rank candidates.
Correct answer is: Binding free energy calculation
Q.41 What type of data is typically stored in the ChEMBL database?
Protein 3D structures
Pharmacological activity data of bioactive molecules
Genetic sequences
Clinical trial protocols
Explanation - ChEMBL curates bioactivity information (IC50, Ki, etc.) for small molecules against various targets.
Correct answer is: Pharmacological activity data of bioactive molecules
Q.42 Which of the following describes the 'lock‑and‑key' model of enzyme catalysis?
The enzyme shape changes to fit the substrate
The enzyme and substrate have complementary shapes that fit without major changes
The enzyme releases the product immediately after binding
The enzyme is a rigid scaffold that rotates upon binding
Explanation - The lock‑and‑key model assumes both enzyme and substrate have fixed shapes that perfectly complement each other.
Correct answer is: The enzyme and substrate have complementary shapes that fit without major changes
Q.43 Which of the following is a typical output of a molecular dynamics trajectory?
A list of protein sequences
Time‑dependent coordinates of atoms
A chemical reaction mechanism
A 2D sketch of the ligand
Explanation - MD outputs coordinates for each frame over time, showing the motion of atoms in the system.
Correct answer is: Time‑dependent coordinates of atoms
Q.44 What does the term 'enantiomer' refer to in stereochemistry?
A molecule with a chiral center and its mirror image
A compound with identical chemical formula but different connectivity
A mixture of isomers
A compound that exists only in the gas phase
Explanation - Enantiomers are stereoisomers that are non‑superimposable mirror images of each other.
Correct answer is: A molecule with a chiral center and its mirror image
Q.45 Which technique is commonly used to validate a docking protocol?
Cross‑validation with known inhibitors
Spectroscopic analysis of the protein
X‑ray crystallography of the docked complex
Thermal shift assay
Explanation - A docking protocol is validated by re‑docking known ligands and comparing predicted poses to crystal structures.
Correct answer is: Cross‑validation with known inhibitors
Q.46 What is the purpose of a 'binding site prediction' algorithm?
To find the most hydrophobic residues
To identify potential ligand‑binding pockets on a protein
To determine the protein’s primary sequence
To calculate the pKa of all residues
Explanation - Binding site prediction algorithms analyze protein surfaces to locate cavities that can accommodate ligands.
Correct answer is: To identify potential ligand‑binding pockets on a protein
Q.47 Which of the following is NOT a commonly used scoring function in docking?
ChemScore
GoldScore
Lipinski's rule of five
AutoDock Vina score
Explanation - Lipinski's rule predicts drug‑likeness; it is not a docking scoring function.
Correct answer is: Lipinski's rule of five
Q.48 In pharmacokinetics, what does the 'half‑life' of a drug represent?
The time it takes for half of the drug to be eliminated
The time to reach maximum concentration
The duration of the drug’s therapeutic effect
The time required for the drug to be absorbed
Explanation - Half‑life is the time needed for the plasma concentration of a drug to reduce by 50 %.
Correct answer is: The time it takes for half of the drug to be eliminated
Q.49 Which type of simulation allows for the exploration of ligand binding pathways?
Steered molecular dynamics (SMD)
Quantum tunneling simulations
Docking only
Pharmacophore modeling
Explanation - SMD applies external forces to a ligand to probe its pathway into or out of a binding site.
Correct answer is: Steered molecular dynamics (SMD)
Q.50 What does the term 'enrichment factor' describe in virtual screening?
The speed of the screening process
The proportion of actives recovered compared to random selection
The number of compounds screened per hour
The computational cost of a docking run
Explanation - Enrichment factor quantifies how much better a screening method is at retrieving active compounds than random chance.
Correct answer is: The proportion of actives recovered compared to random selection
Q.51 Which computational method would you use to predict the pKa of ionizable residues in a protein?
Molecular dynamics
PropKa
AutoDock Vina
Pharmacophore modeling
Explanation - PropKa is a fast tool that estimates pKa values for residues based on their environment.
Correct answer is: PropKa
Q.52 Which of the following describes the 'induced fit' model of enzyme–ligand interaction?
Both enzyme and ligand remain rigid
The ligand induces a conformational change in the enzyme upon binding
The enzyme changes shape to fit a pre‑formed ligand
The ligand and enzyme form a covalent bond immediately
Explanation - Induced fit proposes that binding triggers structural adjustments in the enzyme to accommodate the ligand.
Correct answer is: The ligand induces a conformational change in the enzyme upon binding
Q.53 What is the purpose of a 'solvent accessible surface area' (SASA) calculation?
To predict the binding free energy
To determine the number of rotatable bonds
To estimate which residues are exposed to solvent
To calculate the molecular weight
Explanation - SASA measures the surface area of a protein that is accessible to solvent, important for understanding interactions.
Correct answer is: To estimate which residues are exposed to solvent
Q.54 Which of the following best describes a 'virtual ligand library'?
A physical collection of synthesized compounds
A database of computationally generated small molecules
A list of protein targets
A set of crystallographic structures
Explanation - A virtual library contains digital representations of many potential ligands for in silico screening.
Correct answer is: A database of computationally generated small molecules
Q.55 What does the 'pocket lining residue' refer to in protein–ligand interactions?
Residues that form the walls of the binding cavity
Residues that are mutated in disease
Residues on the protein surface far from the pocket
Residues that are part of the catalytic site only
Explanation - Pocket lining residues define the environment and chemical properties of the binding site.
Correct answer is: Residues that form the walls of the binding cavity
Q.56 Which of these descriptors measures the topological polar surface area (tPSA)?
A sum of contributions from polar atoms
A measure of molecular weight
A count of hydrogen bond donors
The number of aromatic rings
Explanation - tPSA is calculated by summing the surface areas of polar atoms (oxygen, nitrogen, etc.) in the molecule.
Correct answer is: A sum of contributions from polar atoms
Q.57 Which of the following is a primary advantage of using a 3D similarity search over a 2D search?
It is faster computationally
It can capture spatial arrangement of features
It requires less memory
It is more accurate for all cases
Explanation - 3D similarity considers the spatial positioning of substructures, providing a richer comparison than 2D fingerprints.
Correct answer is: It can capture spatial arrangement of features
Q.58 What does the term 'ensemble docking' refer to?
Docking a ligand into multiple receptor conformations
Docking multiple ligands into one receptor
Docking the same ligand multiple times into the same conformation
Docking without considering receptor flexibility
Explanation - Ensemble docking uses an ensemble of protein structures to account for flexibility during ligand binding.
Correct answer is: Docking a ligand into multiple receptor conformations
Q.59 Which computational technique is used to predict the likely binding mode of a ligand to a protein when no crystal structure is available?
Homology modeling of the protein
Molecular mechanics force field
Quantum Monte Carlo
NMR spectroscopy
Explanation - A homology model provides a structural template for docking when experimental structures are missing.
Correct answer is: Homology modeling of the protein
Q.60 In the context of molecular docking, what does the 'grid box' represent?
The region of space where docking is performed
The boundary of the entire protein
The region around the ligand's initial coordinates
The solvent boundary of the system
Explanation - A grid box defines the search space around the binding site where the docking algorithm places the ligand.
Correct answer is: The region of space where docking is performed
Q.61 Which of the following best describes the 'ligand efficiency' metric?
Binding free energy divided by the number of atoms
Number of hydrogen bonds per heavy atom
Binding free energy divided by ligand molecular weight
Binding free energy divided by the number of rotatable bonds
Explanation - Ligand efficiency normalizes binding energy by molecular weight, aiding comparison across different sized molecules.
Correct answer is: Binding free energy divided by ligand molecular weight
Q.62 Which of the following is an example of a non‑covalent interaction important for ligand binding?
Peptide bond
Hydrogen bond
Covalent bond to a cysteine
Phosphodiester bond
Explanation - Non‑covalent interactions such as hydrogen bonds, hydrophobic contacts, and π‑π stacking are crucial for binding affinity.
Correct answer is: Hydrogen bond
Q.63 What is the main purpose of a 'binding pocket characterization' step in drug design?
To identify potential drug targets in the genome
To describe the physicochemical properties of the pocket
To measure the protein's thermal stability
To compute the protein's amino acid sequence
Explanation - Characterization includes size, shape, hydrophobicity, and charge, guiding ligand design.
Correct answer is: To describe the physicochemical properties of the pocket
Q.64 Which of the following best represents the term 'molecular descriptor' in QSAR?
A physical or chemical property that can be calculated from the molecular structure
A method for measuring binding affinity
An algorithm for protein folding
A type of laboratory assay
Explanation - Descriptors translate structural information into numerical values used in QSAR models.
Correct answer is: A physical or chemical property that can be calculated from the molecular structure
Q.65 Which of the following is a key output of a docking program?
Protein sequence alignment
Binding pose and score
NMR spectra
Crystallographic electron density map
Explanation - Docking programs predict how a ligand fits in the binding site and provide a score indicating predicted affinity.
Correct answer is: Binding pose and score
Q.66 Which of the following is a common approach for handling ligand protonation states in docking?
Ignoring protonation states entirely
Generating all possible protonation states and docking each
Using only the neutral form of the ligand
Docking only the charged form
Explanation - Different protonation states can significantly affect docking results; generating and evaluating them improves accuracy.
Correct answer is: Generating all possible protonation states and docking each
Q.67 Which of these is a typical step in the drug discovery pipeline after initial virtual screening?
Patent filing
In vitro potency testing
Synthesis of the target protein
Gene sequencing
Explanation - Validated hits from virtual screening are usually synthesized and tested experimentally for activity.
Correct answer is: In vitro potency testing
Q.68 What is the purpose of a 'grid-based' scoring function in docking?
To compute the binding free energy from molecular dynamics trajectories
To evaluate the fit of a ligand into a pre‑computed grid of potential values
To predict the pKa of the ligand
To visualize the protein’s surface
Explanation - Grid‑based functions speed up calculations by pre‑computing interaction energies on a spatial grid.
Correct answer is: To evaluate the fit of a ligand into a pre‑computed grid of potential values
Q.69 Which of the following best describes the 'thermodynamic cycle' used in binding free energy calculations?
A method to compute the Gibbs free energy change of binding by combining multiple steps
A diagram of the protein folding pathway
An algorithm to predict ligand solubility
A chart showing protein secondary structure content
Explanation - The thermodynamic cycle allows indirect calculation of binding free energies by summing known quantities.
Correct answer is: A method to compute the Gibbs free energy change of binding by combining multiple steps
Q.70 Which of the following best defines the 'drug‑like' property according to Lipinski?
High polar surface area and low logP
Molecular weight < 500 Da, logP < 5, HBD ≤ 5, HBA ≤ 10
Presence of a metal center
Only natural product structures
Explanation - Lipinski’s rule of five predicts oral bioavailability by setting thresholds for key physicochemical properties.
Correct answer is: Molecular weight < 500 Da, logP < 5, HBD ≤ 5, HBA ≤ 10
Q.71 Which of the following best describes the role of a 'solvation model' in docking?
It provides a representation of solvent effects during ligand binding
It defines the chemical formula of the ligand
It predicts the protein's primary sequence
It calculates the electronic structure of the ligand
Explanation - Solvation models approximate the influence of water or other solvents on binding energetics.
Correct answer is: It provides a representation of solvent effects during ligand binding
Q.72 Which of the following is NOT a common source of structural data for proteins?
X‑ray crystallography
Nuclear magnetic resonance (NMR)
Mass spectrometry
Cryo‑electron microscopy (cryo‑EM)
Explanation - Mass spectrometry identifies protein mass but does not provide 3D structures like X‑ray, NMR, or cryo‑EM.
Correct answer is: Mass spectrometry
Q.73 In ligand-based virtual screening, which of the following methods is used to evaluate the similarity between two compounds?
Tanimoto coefficient
Root‑mean‑square deviation
Docking score
Quantum mechanical energy
Explanation - Tanimoto coefficient quantifies the similarity of binary fingerprints, widely used in ligand-based screening.
Correct answer is: Tanimoto coefficient
Q.74 What is the primary function of a 'protein‑protein docking' algorithm?
To predict the binding mode of a small molecule to a protein
To model the interaction between two protein chains
To predict the protein's secondary structure
To analyze ligand pharmacophore features
Explanation - Protein‑protein docking predicts how two proteins interact to form complexes, critical for understanding signaling pathways.
Correct answer is: To model the interaction between two protein chains
Q.75 Which of the following best defines the term 'binding affinity'?
The number of hydrogen bonds in a complex
The strength of the interaction between ligand and protein
The rate of ligand diffusion
The mass of the ligand
Explanation - Binding affinity reflects how tightly a ligand binds to its target, often expressed as Ki or IC50.
Correct answer is: The strength of the interaction between ligand and protein
Q.76 Which computational technique is used to predict the 3D conformation of a small molecule from its SMILES string?
Conformer generation algorithms
Molecular docking
Sequence alignment
Pharmacophore modeling
Explanation - Conformer generators produce low‑energy 3D structures from a 2D representation like SMILES.
Correct answer is: Conformer generation algorithms
Q.77 Which of the following is a key difference between 'rigid' and 'flexible' docking?
Rigid docking allows ligand flexibility, flexible docking does not
Flexible docking allows protein flexibility, rigid docking does not
Rigid docking treats both protein and ligand as rigid, flexible docking allows one or both to flex
There is no difference; both use the same algorithm
Explanation - Rigid docking assumes a fixed receptor, whereas flexible docking accommodates conformational changes.
Correct answer is: Rigid docking treats both protein and ligand as rigid, flexible docking allows one or both to flex
Q.78 In the context of drug discovery, what does the term 'lead candidate' refer to?
A protein that has been identified as a therapeutic target
A compound that shows desirable potency and drug‑like properties
The first synthesized compound in a series
A computational model of a protein target
Explanation - Lead candidates are molecules selected for further optimization based on activity and pharmacokinetic profiles.
Correct answer is: A compound that shows desirable potency and drug‑like properties
Q.79 Which of the following best describes the 'Molecular Operating Environment' (MOE) software?
A web-based platform for sequence alignment
A suite of tools for computational chemistry and drug design
A database of protein structures
A quantum mechanical simulation package
Explanation - MOE integrates modeling, docking, and QSAR tools, widely used in medicinal chemistry.
Correct answer is: A suite of tools for computational chemistry and drug design
Q.80 Which of the following describes a 'virtual screening hit'?
A compound that was found in a commercial library but shows no activity
A compound that passed computational screening and shows potential activity
A protein that binds to a ligand with high affinity
A computational model that fails to predict binding
Explanation - Hits are top candidates from virtual screening that are taken forward for experimental testing.
Correct answer is: A compound that passed computational screening and shows potential activity
Q.81 In molecular dynamics, what is the role of the 'pressure coupling' algorithm?
To maintain a constant temperature
To maintain a constant pressure
To integrate Newton's equations of motion
To calculate binding free energies
Explanation - Pressure coupling adjusts the system's volume to keep pressure constant during an MD simulation.
Correct answer is: To maintain a constant pressure
Q.82 Which of the following best defines 'protein flexibility' in docking?
The ability of the protein to change shape upon ligand binding
The number of hydrogen bonds a protein can form
The rigidity of the ligand
The protein’s secondary structure content
Explanation - Protein flexibility refers to conformational changes that can influence binding site geometry.
Correct answer is: The ability of the protein to change shape upon ligand binding
Q.83 What is a key advantage of using a 'pharmacophore model' over simple similarity searching?
It requires no known active compounds
It can guide the design of new molecules with desired features
It is computationally faster
It does not require 3D structures
Explanation - Pharmacophore models describe the spatial arrangement of features, enabling the design of novel compounds.
Correct answer is: It can guide the design of new molecules with desired features
Q.84 Which of the following is a commonly used metric for assessing the quality of a homology model?
Root‑mean‑square deviation (RMSD) compared to a crystal structure
The number of atoms in the model
The total charge of the protein
The melting temperature
Explanation - RMSD measures structural similarity between a homology model and a known reference structure.
Correct answer is: Root‑mean‑square deviation (RMSD) compared to a crystal structure
Q.85 In a docking protocol, which step typically follows the initial placement of the ligand?
Protein sequence alignment
Scoring and ranking of poses
Experimental validation
Synthesis of the ligand
Explanation - After docking, each pose is evaluated with a scoring function to predict binding affinity.
Correct answer is: Scoring and ranking of poses
Q.86 Which of the following describes the 'molecular docking score'?
A measure of the number of rotatable bonds in the ligand
A numerical estimate of the ligand's binding affinity
The time required to run the docking simulation
The pKa of the ligand
Explanation - Docking scores approximate how strongly a ligand binds; more negative scores usually indicate stronger binding.
Correct answer is: A numerical estimate of the ligand's binding affinity
Q.87 Which of the following is NOT a typical output of a pharmacophore search?
List of candidate molecules that match the model
Binding free energy predictions
Ranking of matches by similarity score
Visualization of the pharmacophore features
Explanation - Pharmacophore searches identify structural matches; they do not directly predict binding energies.
Correct answer is: Binding free energy predictions
Q.88 Which of the following best explains 'protein–ligand interaction fingerprints' (PLIFs)?
A method to visualize the 3D structure of proteins
A binary representation of interactions between a protein and a ligand
A set of SMILES strings for ligands
A technique for measuring protein solubility
Explanation - PLIFs encode contacts such as hydrogen bonds and hydrophobic interactions, useful for clustering and analysis.
Correct answer is: A binary representation of interactions between a protein and a ligand
Q.89 Which of the following is a common use of 'Monte Carlo simulations' in drug design?
To predict the solubility of a ligand
To sample ligand conformational space stochastically
To perform sequence alignment of proteins
To calculate the melting temperature of a compound
Explanation - Monte Carlo methods generate random samples to explore conformational landscapes of molecules.
Correct answer is: To sample ligand conformational space stochastically
Q.90 Which of the following best describes a 'grid‑free' docking algorithm?
An algorithm that does not pre‑compute a spatial grid for scoring
An algorithm that uses only 2D information
An algorithm that ignores protein flexibility
An algorithm that requires a crystallographic structure
Explanation - Grid‑free docking evaluates interactions directly on-the-fly without using a pre‑computed grid.
Correct answer is: An algorithm that does not pre‑compute a spatial grid for scoring
Q.91 Which of the following best explains the term 'binding mode'?
The orientation and pose of a ligand in the binding pocket
The kinetic rate of ligand dissociation
The protein’s secondary structure
The ligand’s molecular weight
Explanation - Binding mode describes how a ligand is positioned and oriented relative to the binding site.
Correct answer is: The orientation and pose of a ligand in the binding pocket
Q.92 What is the main purpose of the 'H-bond donor count' descriptor?
To predict the compound's solubility
To count the number of hydrogen bond donors in a molecule
To determine the number of rotatable bonds
To calculate the molecular weight
Explanation - The H‑bond donor count is a simple descriptor used in QSAR and drug‑likeness assessments.
Correct answer is: To count the number of hydrogen bond donors in a molecule
Q.93 Which of the following is a key feature of the 'Induced Fit Docking' (IFD) protocol?
It keeps the protein rigid during docking
It allows side‑chain re‑packing after initial pose generation
It uses only 2D chemical features
It excludes solvation effects
Explanation - Induced Fit Docking iteratively adjusts side‑chain conformations to improve ligand fit.
Correct answer is: It allows side‑chain re‑packing after initial pose generation
Q.94 Which of the following best describes the 'Binding Energy Landscape' concept?
A 2D plot of protein secondary structure
A representation of all possible binding energies across a conformational space
A diagram of the protein’s genetic regulation
A table of ligand pharmacokinetics
Explanation - The binding energy landscape maps how binding free energy changes with ligand and protein conformations.
Correct answer is: A representation of all possible binding energies across a conformational space
Q.95 In virtual screening, what is a 'false positive'?
A compound predicted to be active but is inactive experimentally
A compound that is actually active but predicted inactive
A compound that is not part of the library
A compound with high solubility
Explanation - False positives are hits that do not show real activity in subsequent assays.
Correct answer is: A compound predicted to be active but is inactive experimentally
Q.96 Which of the following best explains the term 'flexible ligand docking'?
Docking where the ligand is treated as a rigid body
Docking where ligand torsions are allowed to change
Docking that excludes protein flexibility
Docking that uses a fixed binding site
Explanation - Flexible ligand docking permits rotation around rotatable bonds, improving pose predictions.
Correct answer is: Docking where ligand torsions are allowed to change
Q.97 Which of the following is a typical input for a docking simulation?
Protein sequence in FASTA format
3D structure of the protein in PDB format
SMILES string of the ligand only
Pharmacophore model only
Explanation - Docking requires a 3D representation of both receptor and ligand for accurate modeling.
Correct answer is: 3D structure of the protein in PDB format
Q.98 Which of the following best describes the 'pharmacophore mapping' step?
Aligning 3D structures of multiple proteins
Overlaying ligand features onto a target receptor to identify key interactions
Predicting the 2D structure of a compound
Measuring the solubility of a ligand
Explanation - Pharmacophore mapping positions known active features onto the protein to guide design.
Correct answer is: Overlaying ligand features onto a target receptor to identify key interactions
Q.99 Which of the following best explains the concept of 'ligand efficiency' (LE)?
The ratio of ligand weight to the number of hydrogen bonds
Binding free energy per heavy atom
The speed of ligand synthesis
The number of rotatable bonds per unit mass
Explanation - LE normalizes binding affinity by ligand size, enabling comparison across different molecular weights.
Correct answer is: Binding free energy per heavy atom
Q.100 Which of the following is a common type of 'fragment‑based drug design'?
Screening large libraries of full molecules
Using small chemical fragments to build up a lead
Focusing only on pharmacokinetic properties
Designing drugs based on gene sequencing data
Explanation - Fragment-based design identifies small, low‑affinity fragments that can be chemically linked or grown into potent ligands.
Correct answer is: Using small chemical fragments to build up a lead
Q.101 Which of the following is NOT an output of a typical docking run?
Docking pose coordinates
Binding affinity score
Protein crystal structure
Ranking of poses
Explanation - Docking uses the protein structure as input; it does not produce a new crystal structure.
Correct answer is: Protein crystal structure
Q.102 Which of the following best describes the 'Monte Carlo Free Energy Perturbation' (MCFEP) method?
A technique to compute the change in free energy between two ligands via stochastic sampling
A method to predict ligand solubility
A tool for visualizing protein structures
An algorithm for aligning protein sequences
Explanation - MCFEP uses Monte Carlo sampling to estimate free‑energy differences for ligand transformations.
Correct answer is: A technique to compute the change in free energy between two ligands via stochastic sampling
Q.103 Which of the following best explains the 'binding pocket volume' calculation?
It measures the surface area of the protein
It quantifies the size of the cavity that can accommodate a ligand
It counts the number of hydrogen bonds in the protein
It calculates the protein's melting temperature
Explanation - Pocket volume is the spatial space available within the binding site for ligand occupancy.
Correct answer is: It quantifies the size of the cavity that can accommodate a ligand
Q.104 Which of the following best defines 'molecular mechanics force field parameters'?
Values used to calculate electronic energies via quantum mechanics
Parameters that define bond stretching, angle bending, torsion, and non‑bonded interactions
The number of atoms in the ligand
The pKa of the protein residues
Explanation - Force field parameters are numerical values used in classical potential energy functions.
Correct answer is: Parameters that define bond stretching, angle bending, torsion, and non‑bonded interactions
Q.105 Which of the following is a key advantage of using 'QM/MM' over pure molecular mechanics for protein–ligand studies?
It is computationally cheaper
It can accurately describe electronic effects in the binding site
It does not require a protein structure
It eliminates the need for solvation models
Explanation - QM/MM treats the active site with quantum mechanics, capturing bond formation/breaking accurately.
Correct answer is: It can accurately describe electronic effects in the binding site
Q.106 Which of the following best describes the 'pocket shape complementarity'?
The ability of the ligand to change shape to fit the pocket
The match between the geometric shape of the pocket and the ligand
The charge distribution of the pocket
The size of the pocket only
Explanation - Shape complementarity assesses how well the ligand fits into the cavity, influencing binding affinity.
Correct answer is: The match between the geometric shape of the pocket and the ligand
Q.107 Which of the following best explains 'free energy of binding' in the context of molecular docking?
The total energy of the protein alone
The difference in free energy between the bound and unbound states
The energy required to solubilize the ligand
The kinetic energy of the system
Explanation - Binding free energy represents the thermodynamic favorability of the interaction.
Correct answer is: The difference in free energy between the bound and unbound states
Q.108 Which of the following is a common source of protein structural data used in drug design?
The Protein Data Bank (PDB)
The PubChem database
The ChEMBL activity database
The Gene Ontology database
Explanation - PDB contains experimentally determined 3D structures essential for docking and modeling.
Correct answer is: The Protein Data Bank (PDB)
Q.109 Which of the following best describes 'binding site hotspot mapping'?
Identifying residues critical for ligand binding using computational probes
Predicting the melting temperature of the protein
Determining the pKa of all protein residues
Visualizing the secondary structure of the protein
Explanation - Hotspot mapping uses probe molecules to locate energetically favorable binding regions.
Correct answer is: Identifying residues critical for ligand binding using computational probes
Q.110 Which of the following is a primary goal of the 'lead optimization' phase?
To discover new biological targets
To improve potency, selectivity, and drug‑like properties of a lead
To sequence the DNA of the target organism
To perform initial high‑throughput screening
Explanation - Lead optimization refines a hit into a drug‑like candidate through medicinal chemistry.
Correct answer is: To improve potency, selectivity, and drug‑like properties of a lead
Q.111 Which of the following is a key difference between 'pharmacophore modeling' and 'molecular docking'?
Pharmacophore modeling uses 3D structural information while docking does not
Docking requires a protein structure, while pharmacophore modeling can use only ligand data
Docking predicts binding pose, pharmacophore models predict pharmacokinetics
Pharmacophore modeling is always more accurate than docking
Explanation - Pharmacophore modeling is ligand‑centric and does not need a receptor structure, whereas docking needs both.
Correct answer is: Docking requires a protein structure, while pharmacophore modeling can use only ligand data
Q.112 Which of the following best describes the 'Enrichment Factor' in virtual screening?
The ratio of active compounds retrieved to total compounds screened
The ratio of predicted active compounds to the number of inactive compounds
The ratio of active compounds retrieved over random selection
The total number of compounds in the library
Explanation - Enrichment factor compares the performance of a screening method to random chance.
Correct answer is: The ratio of active compounds retrieved over random selection
Q.113 Which of the following is an example of a 'scaffold hop' in medicinal chemistry?
Replacing a side‑chain group with a different functional group
Substituting the core scaffold of a molecule with a different core
Increasing the number of rotatable bonds
Adding a solubilizing group
Explanation - Scaffold hopping changes the core structure while maintaining key pharmacophoric features.
Correct answer is: Substituting the core scaffold of a molecule with a different core
Q.114 What is the main advantage of using 'ensemble docking' over single‑structure docking?
It ignores protein flexibility
It allows docking into multiple receptor conformations to capture flexibility
It is computationally cheaper
It provides exact binding free energies
Explanation - Ensemble docking accounts for protein conformational changes, improving prediction accuracy.
Correct answer is: It allows docking into multiple receptor conformations to capture flexibility
Q.115 Which of the following best explains the concept of 'binding energy decomposition'?
Breaking down the total binding energy into contributions from individual residues or interactions
Computing the total energy of the ligand alone
Calculating the free energy of solvent
Summing the energies of all atoms in the protein
Explanation - Energy decomposition helps identify key residues contributing to binding affinity.
Correct answer is: Breaking down the total binding energy into contributions from individual residues or interactions
Q.116 Which of the following best describes the 'pharmacophore feature' termed 'aromatic ring'?
A hydrophilic group capable of hydrogen bonding
A planar ring of conjugated π electrons
A group that donates a proton
A charged group with a permanent charge
Explanation - Aromatic rings are common pharmacophore features due to their ability to stack and interact via π interactions.
Correct answer is: A planar ring of conjugated π electrons
Q.117 Which of the following best defines a 'protein pocket' in drug design?
A region on the protein surface that is highly hydrophilic
A concave cavity where a ligand can bind
The entire protein sequence
The set of secondary structure elements
Explanation - A pocket is a structural cavity that accommodates ligands, often the target for drug binding.
Correct answer is: A concave cavity where a ligand can bind
Q.118 What does the 'Tanimoto similarity' measure between two molecules?
The difference in molecular weights
The overlap of their binary fingerprint representations
The absolute number of hydrogen bonds they can form
The difference in their 3D shapes
Explanation - Tanimoto similarity calculates the ratio of shared bits over the total number of bits in two fingerprints.
Correct answer is: The overlap of their binary fingerprint representations
Q.119 Which of the following best explains the term 'ligand efficiency index' (LEI)?
Binding free energy per heavy atom of the ligand
Number of hydrogen bond donors per molecular weight
Total number of rotatable bonds per heavy atom
The ratio of ligand weight to number of hydrogen bond acceptors
Explanation - LEI normalizes binding affinity to ligand size, facilitating comparison across different molecules.
Correct answer is: Binding free energy per heavy atom of the ligand
Q.120 Which of the following best describes a 'molecular docking score'?
A measure of the ligand’s solubility
An estimation of the ligand’s binding affinity to the target protein
A measure of the number of rotatable bonds
The ligand’s molecular weight
Explanation - Docking scores are computational estimates of how well a ligand binds to its target.
Correct answer is: An estimation of the ligand’s binding affinity to the target protein
Q.121 Which of the following best defines the 'binding pocket volume' in protein–ligand interactions?
The total number of residues in the protein
The spatial space inside the pocket that can accommodate a ligand
The number of hydrogen bonds that can be formed
The total surface area of the protein
Explanation - Binding pocket volume refers to the size of the cavity that can host a ligand.
Correct answer is: The spatial space inside the pocket that can accommodate a ligand
Q.122 Which of the following best describes a 'pharmacophore'?
A 3D arrangement of steric and electronic features necessary for biological activity
A chemical reaction mechanism
A type of protein fold
A method for measuring protein concentration
Explanation - A pharmacophore captures the essential features required for ligand binding.
Correct answer is: A 3D arrangement of steric and electronic features necessary for biological activity
Q.123 What is the primary purpose of a 'virtual ligand library' in drug discovery?
To store physical samples of compounds
To provide a collection of digital representations of potential ligands for computational screening
To catalog protein structures
To store experimental assay data
Explanation - Virtual libraries allow rapid in silico screening of thousands to millions of compounds.
Correct answer is: To provide a collection of digital representations of potential ligands for computational screening
Q.124 Which of the following is an example of a 'grid‑based' scoring function used in docking?
AutoDock Vina
Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA)
Quantum mechanics
Molecular Dynamics simulation
Explanation - AutoDock Vina uses a grid‑based approach to calculate interaction energies efficiently.
Correct answer is: AutoDock Vina
Q.125 Which of the following best explains the term 'binding affinity' in drug discovery?
The rate at which a drug is absorbed
The strength of the interaction between a ligand and its target protein
The rate of drug metabolism
The concentration of drug in blood plasma
Explanation - Binding affinity is a measure of how strongly a ligand binds to its target; lower Kd or Ki indicates higher affinity.
Correct answer is: The strength of the interaction between a ligand and its target protein
Q.126 Which of the following best describes the 'hydrogen bond donor count' descriptor?
The number of hydrogen atoms attached to heteroatoms that can donate a hydrogen bond
The total number of hydrogen atoms in the molecule
The number of acceptors in the molecule
The number of rotatable bonds
Explanation - This descriptor counts hydrogen bond donors, which are critical for ligand‑protein interactions.
Correct answer is: The number of hydrogen atoms attached to heteroatoms that can donate a hydrogen bond
Q.127 Which of the following best defines 'molecular dynamics' simulation?
A method to compute electronic structure of molecules
A computational technique that simulates the motion of atoms over time using Newtonian physics
A way to visualize chemical reactions
A process to synthesize molecules in silico
Explanation - MD follows the time evolution of a system, providing insights into conformational changes.
Correct answer is: A computational technique that simulates the motion of atoms over time using Newtonian physics
Q.128 Which of the following best explains the term 'binding pocket lining residue'?
Residues that are located on the surface far from the binding site
Residues that form the walls of the binding pocket
Residues that are mutated in disease
Residues that are part of the catalytic site only
Explanation - Pocket lining residues define the environment and chemical properties of the binding site.
Correct answer is: Residues that form the walls of the binding pocket
Q.129 Which of the following best defines a 'solvent accessible surface area' (SASA) calculation?
It estimates the number of hydrogen bonds the ligand can form
It quantifies the surface area of a protein exposed to solvent
It calculates the protein's molecular weight
It determines the number of rotatable bonds
Explanation - SASA is used to assess solvent exposure and to predict interaction hotspots.
Correct answer is: It quantifies the surface area of a protein exposed to solvent
Q.130 What is the primary function of a 'grid box' in docking simulations?
To define the search space where the ligand will be positioned
To determine the number of rotatable bonds in a ligand
To calculate the protein’s melting temperature
To predict the binding free energy
Explanation - The grid box specifies the 3D region around the binding site where the docking algorithm samples ligand poses.
Correct answer is: To define the search space where the ligand will be positioned
Q.131 Which of the following best describes the 'pharmacophore mapping' step?
Overlaying ligand features onto a target receptor to identify key interactions
Predicting the 2D structure of a compound
Measuring the solubility of a ligand
Visualizing the secondary structure of a protein
Explanation - Pharmacophore mapping places known active features onto the protein to guide design.
Correct answer is: Overlaying ligand features onto a target receptor to identify key interactions
Q.132 Which of the following best explains the concept of 'binding mode' in docking?
The orientation and pose of a ligand in the binding pocket
The kinetic rate of ligand dissociation
The protein’s secondary structure
The ligand’s molecular weight
Explanation - Binding mode describes how a ligand is positioned and oriented relative to the binding site.
Correct answer is: The orientation and pose of a ligand in the binding pocket
Q.133 Which of the following best defines a 'molecular descriptor' in QSAR?
A physical or chemical property that can be calculated from the molecular structure
A method to measure binding affinity
An algorithm for protein folding
A laboratory assay technique
Explanation - Descriptors translate structural information into numerical values used in QSAR models.
Correct answer is: A physical or chemical property that can be calculated from the molecular structure
Q.134 Which of the following is a typical output of a pharmacophore search?
List of candidate molecules that match the model
Binding free energy predictions
Ranking of matches by similarity score
Visualization of the pharmacophore features
Explanation - Pharmacophore searches identify compounds that fit the spatial arrangement of key features.
Correct answer is: List of candidate molecules that match the model
Q.135 Which of the following best describes the 'binding energy decomposition' analysis?
Breaking down the total binding energy into contributions from individual residues or interactions
Computing the total energy of the ligand alone
Calculating the free energy of solvent
Summing the energies of all atoms in the protein
Explanation - Energy decomposition helps identify key residues contributing to binding affinity.
Correct answer is: Breaking down the total binding energy into contributions from individual residues or interactions
Q.136 Which of the following best describes a 'molecular dynamics simulation'?
A method to compute electronic structure of molecules
A computational technique that simulates the motion of atoms over time using Newtonian physics
A way to visualize chemical reactions
A process to synthesize molecules in silico
Explanation - MD follows the time evolution of a system, providing insights into conformational changes.
Correct answer is: A computational technique that simulates the motion of atoms over time using Newtonian physics
Q.137 Which of the following best defines the term 'pharmacophore'?
A 3D arrangement of steric and electronic features necessary for biological activity
A chemical reaction mechanism
A type of protein fold
A method for measuring protein concentration
Explanation - A pharmacophore captures the essential features required for ligand binding.
Correct answer is: A 3D arrangement of steric and electronic features necessary for biological activity