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

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Q. Which of the following is untrue about Grid Representation?

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Q. 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.

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Q. In Grid representation, the lowest score represents the best surface complementarity for a given translational scan.

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Q. In Property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking.

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Q. Which of the following is untrue about Hydrophobicity?

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Q. Oligomers are often obligate complexes meaning that the free-energy cost of dissociation is high and they exist as oligomers under physiological conditions.

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Q. Which of the following is untrue about Electrostatic Complementarity?

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Q. Proteins are dynamic entities that undergo _______

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Q. Typical motions of proteins will be primarily treated by a rigid body model for docking.

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Q. In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.

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Q. In 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.

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Q. The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ______ ligand conformations. Where, the N is the number of low-energy conformations.

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

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Q. 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.

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

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

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Q. Which of the following is true regarding Protein flexibility?

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Q. In a similar way to structure prediction methods models can be evaluated using RMSD to measure the similarity between two molecular complexes.

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Q. In case of protein-protein docking, the level of success is dependent on the system under study.

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