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Bioinformatics Practice Test Questions: Protein Tertiary Structure Prediction
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Avg score: 58% • Most missed: “Which of the following is untrue about Sequence Alignment Step?”

Tertiary protein structure prediction is computational elucidation of the three-dimensional structure of a protein for which experimentally determined structure is unavailable from its amino acid sequence.

Topic include: Ab Initio Protein Structural Prediction & Homology Modeling, & Threading and Fold Recognition.

Bioinformatics Practice Test Questions: Protein Tertiary Structure Prediction
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25 Questions

1. Which of the following is untrue about 3D-PSSM?
2. The prediction programs are thus designed using the energy minimization principle.
3. Which of the following is untrue about profile method?
4. Which of the following is untrue about homology modeling?
5. In Side Chain Refinement step, A side chain can be built by searching every possible conformation at every torsion angle of the side chain to select the one that has the lowest interaction energy with neighboring atoms.
6. Threading or structural fold recognition predicts the structural fold of an unknown protein sequence by fitting the sequence into a structural database and selecting the best-fitting fold.
7. Which of the following is untrue about specialized programs for loop modeling?
8. The procedure begins by measuring the orientation and distance of the anchor regions in the stems and searching PDB for segments of the same length that also match the above endpoint conformation.
9. In the pairwise energy based method, a protein sequence is searched for in a structural fold database to find the best matching structural fold using ______ criteria.
10. In Rosetta, The segments with assigned _______ structures are subsequently assembled into a ______ dimensional configuration.
11. There are a large number of protein folds available, compared to millions of protein sequences.
12. Rosetta is a web server that predicts protein three-dimensional conformations using the ab initio method.
13. Which of the following is untrue about threading and fold recognition?
14. Which of the following is untrue about Backbone Model Building Step?
15. In the step of Model Refinement Using Energy Function, the structural irregularities can be corrected by applying the energy minimization procedure on the entire model, which moves the atoms in such a way that the overall conformation has the lowest energy potential.
16. The next step in the pairwise energy based method is to build a crude model for the target sequence by replacing aligned residues in the template structure with the corresponding residues in the query.
17. Which of the following is untrue about Ab initio prediction?
18. Which of the following is true about Gen Threader?
19. Which of the following is untrue about Loop Modeling Step?
20. Energy minimization has to be used with caution because excessive energy minimization often moves residues away from their correct positions.
21. Which of the following is untrue about template Selection Step?
22. Which of the following is untrue about Sequence Alignment Step?
23. The algorithms used here can be classified into two categories, pairwise energy based and profile based.
24. Searching for a fold with the absolute minimum energy may not be valid in reality.
25. Because threading and fold recognition detect structural homologs ________ relying on sequence similarities, they have been shown to be _______ than PSI-BLAST in finding distant evolutionary relationships

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