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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Q. There was little degree of success in docking an antibody-antigen complex in the second challenge for the protein-protein docking evaluation.

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Q. The ______ is an ongoing community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction.

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Q. An understanding of the importance of different factors in a particular interaction is important if confidence in the results is required. Which of the following are not those factors?

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Q. Information about shape, hydrophobicity, electrostatics, evolutionary relationships and conformational flexibility is not always available and the search for a universally applicable scoring function as well as an adequate treatment of conformational flexibility is ongoing.

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Q. In practical circumstances there exists an experimental structure of the complex.

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Q. Visualization methods are very important in viewing molecular properties on molecules. Of particular note is the rendering of molecular surfaces according to their various properties (that can be expressed numerically).

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Q. The popular program RasMol can be made to view molecular properties by assigning those properties to the temperature factor column of the sdf file in question only.

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Q. The GRASP and VRLM have been incorporated into the GRASS server.

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