MM4MX Multiple-choice Test

1. What do the letters M.O.E. stand for?

  1. Molecular Operating Engine
  2. Modular Operating Engine
  3. Molecular Operating Environment
  4. Montreal Omnibus Executive

2. When using MOE, on a standard 3-button mouse, which button do you click to select an atom?

  1. The left one
  2. The middle one
  3. The right one
  4. None of them - you press the Enter key on the keyboard.

3. MOE can map out the inside of a protein binding site with hydrophilic and hydrophobic preference volumes by combining contact statistics. But which of these other programs does much the same thing?

  1. GOLD
  2. IsoStar
  3. SuperStar
  4. MultiMap

4. MOE's data hierarchy has four levels; what comes below the System and above Residues?

  1. Domains
  2. Chains
  3. Proteins
  4. Quarks

5. Which of the following could be used to run MD simulations of DNA:

  1. Diamond
  2. GOLD
  3. AMBER
  4. GRID

6. In the current world of DNA simulation, how long is a piece of string?

  1. 10 ps
  2. 5 ns
  3. 100 ns
  4. 3.4 angstroms

7. Which of the following is a new CCP to support Biomolecular Simulation?

  1. CCPSim
  2. CCPX
  3. CCP99
  4. CCPB

8. The main cause of false positives in Structure-based Virtual Screening is:

  1. Not known
  2. Free energy of solvation not being estimated accurately
  3. Poor parameters for scoring functions
  4. Motion of protein side-chains
  5. Ligand conformational freedom

9. Pharmacophore constraints speed up docking because:

  1. The number of ligand conformations processed is reduced
  2. The number of docked orientations (or poses) is reduced
  3. The time for geometry refinement is reduced
  4. The number of ligand conformations and docked orientations is reduced

10. The percentage of false postives in Structure-based Virtual Screening software is typically:

  1. >75%
  2. 50-75%
  3. 25-50%
  4. < 25%

11. Which of the following statements is NOT true:

  1. Docking algorithms are suitable for parallel computing
  2. Energy calculations are theoretically better than empirical scoring functions such as ChemScore
  3. Free energy perturbation calculations are very time-consuming
  4. Knowledge based scoring functions ignore fundamental theory
  5. Geometry refinement of the ligand is a necessary step to obtain the most accurate results

12. What is the conventional CCP4MG format for specifying the CA atom of residue 27?

  1. 27CA
  2. 27/CA
  3. ///27/CA
  4. (i; 27) & (n; CA)

13. A simple harmonic potential can be used to approximate the stretching behaviour of a chemical bond. Which one of the following is false?

  1. It models equilibrium behaviour well.
  2. At long distances the function inverts.
  3. The zero-point energy of the bond is neglected.
  4. The force constants used do not represent the real stretching force for a given bond.

14. Which one of the following statements is true?

  1. Long range electrostatic interactions are unimportant when modelling biological systems.
  2. It is valid to separate the different components of a force field and interpret the energies on this basis.
  3. Van der Waals interactions take place between all types of chemical groups, both polar and non-polar.
  4. Aromatic rings prefer a face-to-face interaction.

15. In energy minimization it is common to use gradient methods. Which one of the following is false?

  1. The search direction followed is determined by the forces within the system.
  2. The most rigorous methods require knowledge of the derivative of force.
  3. Minimisation algorithms always locate the global energy minimum on the energy hypersurface.
  4. Close to the minimum steepest descents shows poor convergence behaviour.

16. Which one of the following statements about docking algorithms is false?

  1. Docking methods will typically provide a unique solution.
  2. Docking methods incorporating protein flexibility are commonplace.
  3. Exploring search space is only a minor computational overhead.
  4. Crystal structures of complexes are still the best validation methods for docking methods.

17. Multiscale methods use which of these methods?

  1. Molecular structures are divided up and the atomic properties are allocated to feature points.
  2. Energy minimization of all points is required at each stage in the docking process.
  3. In every generation of the calculation search space is decreased.
  4. The intermolecular interactions are calculated using simple electrostatic and van der Waals potentials.

18. Which one of the following is true?

  1. Plant cells do not require glutamate for ion transport.
  2. Both glutamate and glycine are required for the plant ion transporters to function.
  3. Plant glutamate and glycine receptors are unrelated to those in mammalian sytems.
  4. Plants do not contain the amino acid glycine.

19. In the practical application of molecular dynamcis simulations which fundamental equation is used:

  1. Law of gravity
  2. Schrödinger equation from quantum mechanics
  3. Newton's equation of motion
  4. Thermodynamic equations of state

20. Truncation is applied to which component of the potential energy function

A.eq1
B.eq2
C.eq3
D.eq4

21. Molecular dynamics simulations can be used to

  1. Follow the time dependence of a biomolecule
  2. Calculate thermodynamics quantitites
  3. Calculate spectroscopic quantities
  4. Dock ligands
  5. All of the above
  6. None of the above

22. The trajectory in a molecular dynamics simulation of your typical biomolecule results from an analytical solution of the appropriate equations

  1. True
  2. False It results from a numerical integration of the appropriate equations

23. The temperature in a molecular dynamics simulation is directly related to the atomic velocity

  1. True
  2. False

24. Which of the following is a semiempirical quantum chemical molecular orbital method?

  1. PX4
  2. RHF/6-31G*
  3. AM1
  4. CCSD

25. Which of the following are methods typically used to treat the boundary between QM and MM atoms?

  1. Transition states
  2. Link atoms
  3. Generalized hybrid orbitals
  4. Unpaired electrons

26. According to transition state theory there should be a direct, linear relationship between the calculated activation energy and:

  1. kcat
  2. ln kcat
  3. (kcat)2
  4. 1/kcat

27. True or false: the transition state is the highest energy point along the highest energy path between reactants and products

  1. True
  2. False: the transition state is the highest energy point along the lowest energy path between reactants and products

28. QM/MM calculations on enzymes typically include which of the following interactions between QM and MM atoms:

  1. Van der Waals interactions represented by MM Lennard-Jones terms
  2. Electrostatic interactions represented by MM point charges polarizing the QM region
  3. MM bonded interactions between QM and MM atoms in the same molecule

29. Glutathione is a

  1. tripeptide
  2. dipeptide
  3. pentapeptide
  4. tetrapeptide
  5. oligosaccharide