MM4MX Multiple-choice Test
1. What do the letters M.O.E. stand for?
- Molecular Operating Engine
- Modular Operating Engine
- Molecular Operating
- Montreal Omnibus Executive
2. When using MOE, on a standard 3-button mouse, which button do
you click to select an atom?
- The left
- The middle one
- The right one
- 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
4. MOE's data hierarchy has four levels; what comes below the
System and above Residues?
5. Which of the following could be used to run MD simulations of
6. In the current world of DNA simulation, how long is a piece
- 10 ps
- 5 ns
- 100 ns
- 3.4 angstroms
7. Which of the following is a new CCP to support Biomolecular
8. The main cause of false positives in Structure-based Virtual
- Not known
- Free energy of solvation not being estimated accurately
- Poor parameters for scoring functions
- Motion of protein side-chains
- Ligand conformational freedom
9. Pharmacophore constraints speed up docking because:
- The number of ligand conformations processed is reduced
- The number of docked orientations (or poses) is reduced
- The time for geometry refinement is reduced
- The number of ligand
conformations and docked orientations is reduced
10. The percentage of false postives in Structure-based Virtual
Screening software is typically:
- < 25%
11. Which of the following statements is NOT true:
- Docking algorithms are suitable for parallel computing
- Energy calculations are
theoretically better than empirical scoring functions such as
- Free energy perturbation calculations are very
- Knowledge based scoring functions ignore
- 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?
- (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
- It models equilibrium behaviour well.
- At long distances the
- The zero-point energy of the bond is neglected.
- The force constants used do not represent the
real stretching force for a
14. Which one of the following statements is true?
- Long range electrostatic interactions are unimportant when
modelling biological systems.
- It is valid to separate the different components of a force
field and interpret the energies on this basis.
- Van der
Waals interactions take place between all types
of chemical groups, both polar and non-polar.
- 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?
- The search direction followed is determined by the forces
within the system.
- The most rigorous methods require knowledge of the derivative of force.
- Minimisation algorithms
always locate the global energy minimum on the energy
- Close to the minimum steepest descents shows poor convergence
16. Which one of the following statements about docking algorithms is false?
- Docking methods will
typically provide a unique solution.
- Docking methods incorporating protein flexibility are
- Exploring search space is only a minor computational
- Crystal structures of complexes are still the best validation
methods for docking methods.
17. Multiscale methods use which of these methods?
- Molecular structures are divided up and the atomic properties
are allocated to feature points.
- Energy minimization of all
points is required at each stage in the docking
- In every generation of the calculation search space is
- The intermolecular interactions are calculated using simple
electrostatic and van der Waals potentials.
18. Which one of the following is true?
- Plant cells do not require glutamate for ion transport.
- Both glutamate and glycine
are required for the plant ion transporters to
- Plant glutamate and glycine receptors are unrelated to those in
- Plants do not contain the amino acid glycine.
19. In the practical application of molecular dynamcis simulations
which fundamental equation is used:
- Law of gravity
- Schrödinger equation from quantum mechanics
- Newton's equation of
- Thermodynamic equations of state
20. Truncation is applied to which component of the potential
21. Molecular dynamics simulations can be used to
- Follow the time dependence of a biomolecule
- Calculate thermodynamics quantitites
- Calculate spectroscopic quantities
- Dock ligands
- All of the
- None of the above
22. The trajectory in a molecular dynamics simulation of your
typical biomolecule results from an analytical solution of the
- 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
24. Which of the following is a semiempirical quantum chemical
molecular orbital method?
25. Which of the following are methods typically used to treat the
boundary between QM and MM atoms?
- Transition states
- Link atoms
- Generalized hybrid orbitals
- Unpaired electrons
26. According to transition state theory there should be a direct,
linear relationship between the calculated activation energy
- ln kcat
27. True or false: the transition state is the highest energy
point along the highest energy path between reactants and
- 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:
- Van der Waals interactions
represented by MM Lennard-Jones terms
- Electrostatic interactions
represented by MM point charges polarizing the QM
- MM bonded interactions
between QM and MM atoms in the same molecule
29. Glutathione is a