Related InterviewSolutions

• 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.(a) sequence-based(b) structure-based(c) energy-based(d) residue-basedI got this question in an interview.My doubt is from Threading and Fold Recognition in section Protein Tertiary Structure Prediction of Bioinformatics
• Which of the following is untrue about template Selection Step?(a) The first step in protein structural modeling is to select appropriate structural templates(b) This forms the foundation for rest of the modeling process(c) There is no use of heuristic alignment search programs(d) The template selection involves searching the Protein Data Bank (PDB) for homologous proteins with determined structuresI had been asked this question in semester exam.The doubt is from Ab Initio Protein Structural Prediction & Homology Modeling in chapter Protein Tertiary Structure Prediction of Bioinformatics
• 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.(a) True(b) FalseThe question was asked in semester exam.This intriguing question comes from Ab Initio Protein Structural Prediction & Homology Modeling in section Protein Tertiary Structure Prediction of Bioinformatics
• Which of the following is untrue about 3D-PSSM?(a) It is a web-based program that employs the structural profile method to identify protein folds(b) The profiles for each protein superfamily are constructed by combining multiple smaller profiles(c) A protein structural superfamily doesn’t have sequence-based PSI-BLAST profile(d) In initial steps, protein structures in a superfamily based on the SCOP classification are superimposedI have been asked this question by my college professor while I was bunking the class.Origin of the question is Threading and Fold Recognition topic in chapter Protein Tertiary Structure Prediction of Bioinformatics
• Which of the following is untrue about Loop Modeling Step?(a) In the sequence alignment for modeling, there are often regions caused by insertions and deletions producing gaps in sequence alignment(b) In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment(c) The gaps cannot be directly modeled(d) Loop modeling is required for closing the gaps requiresI had been asked this question by my college professor while I was bunking the class.My query is from Ab Initio Protein Structural Prediction & Homology Modeling in portion Protein Tertiary Structure Prediction of Bioinformatics
• Which of the following is true about Gen Threader?(a) It is a web-based program that uses a hybrid of the profile and pairwise energy methods(b) It is a web-based program that uses profile methods only(c) It is a web-based program that uses pairwise energy methods only(d) The initial step is quite dissimilar to 3D-PSSMThe question was asked in exam.The question is from Threading and Fold Recognition topic in division Protein Tertiary Structure Prediction of Bioinformatics
• 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.(a) True(b) FalseThe question was asked in exam.My question is based upon Ab Initio Protein Structural Prediction & Homology Modeling topic in section Protein Tertiary Structure Prediction of Bioinformatics
• Which of the following is untrue about profile method?(a) A profile is constructed for a group of related protein structures(b) The propensity of amino acids in not in picture of this method(c) Statistical information from these aligned residues is then used to construct a profile(d) The structural profile is generated by the superimposition of the structures to expose corresponding residuesI have been asked this question during an online exam.Query is from Threading and Fold Recognition topic in section Protein Tertiary Structure Prediction of Bioinformatics
• Which of the following is untrue about specialized programs for loop modeling?(a) PETRA is a web server that models loops using the database approach(b) FREAD is a web server that models loops using the database approach(c) CODA is a web server that uses a consensus method based on the prediction results from FREAD and PETRA(d) For loops of three to eight residues, CODA uses consensus conformation of both methodsThe question was asked during a job interview.I would like to ask this question from Ab Initio Protein Structural Prediction & Homology Modeling in portion Protein Tertiary Structure Prediction of Bioinformatics
• Which of the following is untrue about Sequence Alignment Step?(a) 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(b) The realignment is the most critical step in homology modeling(c) The realignment directly affects the quality of the final model(d) Errors made in the alignment step can be corrected in the following modeling stepsI had been asked this question in a job interview.My doubt stems from Ab Initio Protein Structural Prediction & Homology Modeling in portion Protein Tertiary Structure Prediction of Bioinformatics