This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Evaluation of Models & Visualization Methods”.
1. In a similar way to structure prediction methods models can be evaluated using RMSD to measure the similarity between two molecular complexes.
a) True
b) False
View Answer
Explanation: This is only the case if an experimental structure already exists. Several docking methods have been evaluated at ‘Critical Assessment of Structure Prediction 2’ (CASP2) for both protein-ligand and protein-protein interactions.
2. In case of protein-protein docking, the level of success is dependent on the system under study.
a) True
b) False
View Answer
Explanation: For the protein-protein docking evaluation several of the same docking methodologies were used in both docking challenges. In the first challenge involving a protein inhibitor all the groups successfully predicted the complex.
3. There was little degree of success in docking an antibody-antigen complex in the second challenge for the protein-protein docking evaluation.
a) True
b) False
View Answer
Explanation: This may be because modeling molecular recognition is in general more difficult in antibody-antigen than protein-inhibitor systems. In the protein-ligand docking challenge at CASP2 there was generally a good level of success, however, again certain targets proved to be problematic.
4. The ______ is an ongoing community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction.
a) Chronological Assignment of Prediction of Interactions (CAPRI)
b) Chronological Assessment of Prediction of Interactions (CAPRI)
c) Critical Assignment of Prediction of Interactions (CAPRI)
d) Critical Assessment of Prediction of Interactions (CAPRI)
View Answer
Explanation: Clearly there is an ongoing need for assessment of methods. There is currently no one universal method or scoring function that will work on all occasions.
5. 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?
a) Shape
b) Hydrophobicity
c) Electrostatics
d) pH
View Answer
Explanation: Not that the parameter pH is not related at all but is quite distinctly related to the mentioned factors. Also, pH is relative to the state of the molecule at given instant, other factors being evolutionary relationships and conformational flexibility.
6. 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.
a) True
b) False
View Answer
Explanation: The technique of virtual screening of small molecule drugs by computer has become commonplace and a very useful tool in narrowing down the very large number of drugs that might need to be screened by experimental methods. In one study virtual screening provided lead compounds where conventional experimental random screening had failed.
7. In practical circumstances there exists an experimental structure of the complex.
a) True
b) False
View Answer
Explanation: In practical circumstances an experimental structure of the complex does not already exist. Some other evaluation criteria are needed. This is by necessity experimental validation. The hypothetical protein-biomolecular complex predicts a mode of interaction between the two molecules that can be tested experimentally.
8. 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).
a) True
b) False
View Answer
Explanation: This approach has been popularized by the GRASP program. Also Virtual Reality Modeling Language (VRML) viewers can provide similar displays.
9. 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.
a) True
b) False
View Answer
Explanation: The popular program RasMol can also be made to view molecular properties by assigning those properties to the temperature factor column of the PDB file in question. The molecules are then best viewed in Spacefill mode, however, the color scheme used is not flexible.
10. The GRASP and VRLM have been incorporated into the GRASS server.
a) True
b) False
View Answer
Explanation: This allows a Web-based interactive exploration of molecules in the PDB allowing the molecular properties to be viewed on the molecular surface. There are also several other popular molecular graphics programs that allow a similar visualization.
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