Bioinformatics Mcqs

Page No. 74

In Grid representation, in a translational scan the mobile molecule B moves through the grid representing the static molecule A and a signal describing shape complementarity, fc, is generated for each mapping. Mathematically the correlation function, fc, of fA and fB is given by ______ where N is the number of grid points along the cubic axes i, j, and k and α, β, and γ are the translational vectors of the mobile molecule B relative to the static one A.


ac = ∑Ni=1,j=1,k=1 (fA,i,j,k * fBi+αj+βk+ɣ)

✓


bfc = ∑Ni=0,j=0,k=0 (fA,i,j,k * fBi+αj+βk+ɣ)

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c fc = ∑Ni=1,j=1,k=1 (fA,0,0,0 * fBi+αj+βk+ɣ)

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dfc = ∑Ni=0,j=0,k=0 (f0,i,j,k * fBi+αj+βk+ɣ)

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View Answer c = ∑Ni=1,j=1,k=1 (fA,i,j,k * fBi+αj+βk+ɣ)

Which of the following is untrue about Grid Representation?


aTo speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements

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bTo speed up the matching process discretizing the 3-dimensional space using a grid is done

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c Discretizing allows very fast computer matching using search methods such as Fourier transform

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dFourier transform is hardly used in computer matching

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View Answer Fourier transform is hardly used in computer matching

The burial of surface area (or the maximization of surface contact) is an approximation of the effect of shape complementarity.


aTrue

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bFalse

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ceither true and false

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dnone of the mentioned

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View Answer True

Which of the following is untrue about Shape Complementarity?


aThe complementarity between two proteins or a protein and ligand can be described by surface contact or overlap

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bThe complementarity between two proteins or a protein and ligand can be described by the overall buried surface area of two molecules in contact

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cThe complementarity between two proteins or a protein and ligand can be described by the number of adjacent surface points (atoms or residues)

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dThe hydrophobic effect barely has impact on protein folding

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View Answer The hydrophobic effect barely has impact on protein folding

Which of the following is untrue about Amino acid conservation?


aIt has been known for some time that conservation of residues at the surface of a protein family is often related to function

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bConservation of residues at the core of a protein family is often related to function

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cThis may be an enzyme active-site or binding site

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dUnlike hydrophobicity or electrostatic potential, displaying residue conservation on the molecular surface has no physical or chemical basis

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View Answer Conservation of residues at the core of a protein family is often related to function

Which of the following is true regarding Protein flexibility?


aMethods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

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bMethods have been described for the introduction of side-chain flexibility to protein-ligand docking only

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cThe Mean Field principle is rarely used in this

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dMethods have been described for the introduction of side-chain flexibility to protein-protein docking only

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View Answer Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

Stochastic methods can guarantee reaching a global optimal solution and the methods are computationally costly in comparison to the other methods.


aTrue

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bFalse

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ceither true and false

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dnone of the mentioned

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View Answer False

Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members.


aTrue

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b False

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ceither true and false

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dnone of the mentioned

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View Answer True

In a Monte Carlo simulation the score (or energy) is calculated at each step and compared to 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 the temperature.


aTrue

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bFalse

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ceither true and false

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dnone of the mentioned

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View Answer True

In Stochastic search methods, they include methods such as Monte Carlo simulation, simulated annealing, Tabu search, genetic algorithms and evolutionary programming.


aTrue

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bFalse

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ceither true and false

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dnone of the mentioned

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View Answer True

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