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This quiz contains multiple-choice problems and answers on ab initio protein structural prediction, threading and fold recognition.
Which of the following is incorrect regarding homology modelling?
Homology modeling predicts protein structures based on sequence homology with known structures
It is also known as comparative modeling
The principle behind it is that if two proteins share a high enough sequence similarity, they are likely to have very similar three-dimensional structures
It does not involve the evolutionary distances anywhere
Which of the following is incorrect regarding the template selection step?
The first step in protein structural modeling is to select appropriate structural templates
This forms the foundation for rest of the modeling process
There is no use of heuristic alignment search programs
The template selection involves searching the Protein Data Bank (PDB) for homologous proteins with determined structures
Which of the following is incorrect regarding the sequence alignment step?
Once the structure with the highest sequence similarity is identified as a template, the full-length sequences of the template and target proteins need to be realigned using refined alignment algorithms to obtain optimal alignment
The realignment is the most critical step in homology modeling
The realignment directly affects the quality of the final model
Errors made in the alignment step can be corrected in the following modeling steps
Which of the following is incorrect regarding the backbone model building step?
Once optimal alignment is achieved, residues in the aligned regions of the target protein can assume a similar structure as the template proteins
Coordinates of the corresponding residues of the template proteins can be simply copied onto the target protein
If the two residues differ, everything other than the backbone atoms can be copied
If the two aligned residues are identical, coordinates of the side chain atoms are copied along with the main chain atoms
Which of the following is incorrect regarding the loop modelling step?
In the modelling sequence alignment, there are often regions caused by insertions and deletions producing gaps
In the modelling sequence alignment, there are no regions producing gaps
The gaps cannot be directly modelled
Loop modelling is required for closing the gaps
Which of the following is incorrect regarding specialized programs for loop modelling?
PETRA is a web server that models loops using the database approach
FREAD is a web server that models loops using the database approach
CODA is a web server that uses a consensus method based on the prediction results from FREAD and PETRA
For loops of three to eight residues, CODA uses consensus conformation of both methods
In the side chain refinement step, a side chain can be built by searching every possible conformation at every torsion angle and selecting the one having the lowest interaction energy with its neighbouring atoms. True or false?
True
False
In the step of model refinement using the energy function, the structural irregularities can be corrected by applying the energy minimization procedure on the entire model, which moves the atoms so that the overall conformation has the lowest energy potential. True or false?
True
False
Energy minimization must be used with caution because excessive energy minimization often moves residues away from their correct positions. True or false?
True
False
Which of the following is incorrect regarding ab initio prediction?
The limited knowledge of protein folding forms the basis of ab initio prediction
The ab initio prediction method attempts to produce all-atom protein models based on sequence information alone without the aid of known protein structures
The ab initio prediction method attempts to produce all-atom protein models based on sequence information alone with some aid of known protein structures
The perceived advantage of this method is that predictions are not restricted by known folds and that novel protein folds can be identified
The prediction programs are designed using the energy minimization principle. True or false?
True
False
Searching for a fold with the absolute minimum energy may not be valid in reality. True or false?
True
False
Rosetta is a web server that predicts three-dimensional protein conformations using the ab initio method. True or false?
True
False
In Rosetta, the segments with assigned __ structures are subsequently assembled into a __ dimensional configuration.
primary, three
secondary, three
secondary, two
primary, three
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. True or false?
True
False
