Ab Initio Protein Structural Prediction & Homology Modeling MCQ

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• In Rosetta, The segments with assigned _______ structures are subsequently assembled into a ______ dimensional configuration.
  ক

  primary, three

  খ

  secondary, three

  গ

  secondary, two

  ঘ

  primary, three
• Rosetta is a web server that predicts protein three-dimensional conformations using the ab initio method.
  ক

  True

  খ

  False
• Searching for a fold with the absolute minimum energy may not be valid in reality.
  ক

  True

  খ

  False
• The prediction programs are thus designed using the energy minimization principle.
  ক

  True

  খ

  False
• Which of the following is untrue about Ab initio prediction?
  ক

  The limited knowledge of protein folding forms the basis of ab initio prediction

  খ

  The ab initio prediction method attempts to produce all-atom protein models based on sequence information alone without the aid of known protein structures

  গ

  The ab initio prediction method attempts to produce all-atom protein models based on sequence information alone with some aid of known protein structures

  ঘ

  The perceived advantage of this method is that predictions are not restricted by known folds and that novel protein folds can be identified
• Energy minimization has to be used with caution because excessive energy minimization often moves residues away from their correct positions.
  ক

  True

  খ

  False
• 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.
  ক

  True

  খ

  False
• 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.
  ক

  True

  খ

  False
• Which of the following is untrue about specialized programs for loop modeling?
  ক

  PETRA is a web server that models loops using the database approach

  খ

  FREAD is a web server that models loops using the database approach

  গ

  CODA is a web server that uses a consensus method based on the prediction results from FREAD and PETRA

  ঘ

  For loops of three to eight residues, CODA uses consensus conformation of both methods
• 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.
  ক

  True

  খ

  False
• Which of the following is untrue about Backbone Model Building Step?
  ক

  Once optimal alignment is achieved, residues in the aligned regions of the target protein can assume a similar structure as the template proteins

  খ

  Coordinates of the corresponding residues of the template proteins can be simply copied onto the target protein

  গ

  If the two residues differ, everything other than the backbone atoms can be copied

  ঘ

  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 untrue about Sequence Alignment Step?
  ক

  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

  খ

  The realignment is the most critical step in homology modeling

  গ

  The realignment directly affects the quality of the final model

  ঘ

  Errors made in the alignment step can be corrected in the following modeling steps
• Which of the following is untrue about template Selection Step?
  ক

  The first step in protein structural modeling is to select appropriate structural templates

  খ

  This forms the foundation for rest of the modeling process

  গ

  There is no use of heuristic alignment search programs

  ঘ

  The template selection involves searching the Protein Data Bank (PDB) for homologous proteins with determined structures