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

View solution

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

View solution

Q. Which of the following is untrue about Hydrophobicity?

View solution

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

View solution

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

View solution

Q. Proteins are dynamic entities that undergo _______

View solution

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

View solution

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

View solution

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.

View solution

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.

View solution

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

View solution

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.

View solution

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

View solution

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

View solution

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

View solution

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

View solution

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

View solution

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

View solution

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

View solution

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?

View solution