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This quiz contains multiple-choice problems on molecular complementarity, conformational flexibility, model evaluation and visualization methods.
Which of the following is incorrect about shape complementarity?
The complementarity between two proteins or a protein and ligand can be described by surface contact or overlap
The complementarity between two proteins or a protein and ligand can be described by the overall buried surface area of two molecules in contact
The complementarity between two proteins or a protein and ligand can be described by the number of adjacent surface points (atoms or residues)
The hydrophobic effect barely has impact on protein folding
The burial of surface area (or the maximization of surface contact) approximates the effect of shape complementarity. True or false?
True
False
Which of the following is incorrect about grid representation?
To speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements
To speed up the matching process discretizing the 3-dimensional space using a grid is done
Discretizing allows very fast computer matching using search methods such as Fourier transform
Fourier transform is hardly used in computer matching
The lowest score represents the best surface complementarity for a given translational scan in grid representation. True or false?
True
False
Which of the following is incorrect about electrostatic complementarity?
The electrostatic properties of biomolecules play an important role in determining interactions
The burial of charged residues at protein-protein/DNA interfaces is thought to be generally net destabilizing with the hydrophobic effect being the primary driving force
Charged groups involved in the biomolecular interface are often stabilized by other polar or oppositely charged groups on the interacting molecule
Charged groups involved in the biomolecular interface are often stabilized by similar polar or same charged groups on the interacting molecule
Which of the following is incorrect about hydrophobicity?
The hydrophobic effect plays a dominant role in the folding of proteins
Hydrophobic residues aggregate away from contact with water
Hydrophobic residues aggregate to form hydrophobic cores with more polar residues
Hydrophobic residues form the solvent accessible surface but restrict the solubility of the protein
In property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking. True or false?
True
False
Proteins are dynamic entities that undergo
Only fluctuation of flexible loop regions about equilibrium positions when in solution
Only limited conformational change of amino acid side-chains when in solution
Both limited conformational change of amino acid side-chains and fluctuation of flexible loop regions about equilibrium positions when in solution
Illimitable or total conformational change of amino acid side-chains when in solution
A rigid body model will primarily treat typical protein motions for docking. True or false?
True
False
In the multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different __ that are computed __ the ligand being docked into the receptor.
low-energy conformations, after
low-energy conformations, prior to
high-energy conformations, prior to
high-energy conformations, after
The disadvantage of the multiple conformation rigid-body method is that the active conformation may be missed due to a minor structural difference not considered in the __ ligand conformations, where N is the number of low-energy conformations.
N +1
N
N2
N/2
In a Monte Carlo simulation, the score (or energy) is calculated at each step and compared with the previous step. The probability of accepting the step is given by __ where ΔE is the difference in energy; kB is Boltzmann’s constant, and T is the temperature. True or false?
True
False
Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members. True or false?
True
False
Which of the following is true regarding protein flexibility?
Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking
Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only
The mean field principle is rarely used in this
Methods have been described for the introduction of side-chain flexibility to protein-protein docking only
Which of the following is incorrect regarding amino acid conservation?
It has been known for some time that conservation of residues at the surface of a protein family is often related to function
Conservation of residues at the core of a protein family is often related to function
This may be an enzyme active-site or binding site
Unlike hydrophobicity or electrostatic potential, displaying residue conservation on the molecular surface has no physical or chemical basis
