1. 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.

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

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

4. 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.

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

6. 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).

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

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

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

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

11. 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.

12. Which of the following is untrue about Shape Complementarity?

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

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

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

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

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

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

19. 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.

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

21. 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.

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

23. Proteins are dynamic entities that undergo _______

24. 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.

25. 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?