Bioinformatics Mcqs

Page No. 35

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.


aTrue

✓


bFalse

✖


ceither true and false

✖


dnone of these

✖


View Answer True

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

✖


bIn the sequence alignment for modeling, there are no regions producing gaps in sequence alignment

✓


c The gaps cannot be directly modeled

✖


dLoop modeling is required for closing the gaps requires

✖


View Answer In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment

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


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

✖


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

✖


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

✓


dIf the two aligned residues are identical, coordinates of the side chain atoms are copied along with the main chain atoms

✖


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

. Which of the following is untrue about Sequence Alignment Step?


aOnce 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

✖


bThe realignment is the most critical step in homology modeling

✖


cThe realignment directly affects the quality of the final model

✖


d Errors made in the alignment step can be corrected in the following modeling steps

✓


View Answer Errors made in the alignment step can be corrected in the following modeling steps

Which of the following is untrue about template Selection Step?


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

✖


bThis forms the foundation for rest of the modeling process

✖


cThere is no use of heuristic alignment search programs

✓


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

✖


View Answer There is no use of heuristic alignment search programs

. Which of the following is untrue about homology modeling?


aHomology modeling predicts protein structures based on sequence homology with known structures

✖


b It is also known as comparative modeling

✖


cThe principle behind it is that if two proteins share a high enough sequence similarity, they are likely to have very similar three-dimensional structures

✖


dIt doesn’t involve the evolutionary distances anywhere

✓


View Answer It doesn’t involve the evolutionary distances anywhere

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

✓


bIt is a web-based program that uses profile methods only

✖


cIt is a web-based program that uses pairwise energy methods only

✖


d The initial step is quite dissimilar to 3D-PSSM

✖


View Answer It is a web-based program that uses a hybrid of the profile and pairwise energy methods

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

✖


bThe profiles for each protein superfamily are constructed by combining multiple smaller profiles

✖


cA protein structural superfamily doesn’t have sequence-based PSI-BLAST profile

✓


dIn initial steps, protein structures in a superfamily based on the SCOP classification are superimposed

✖


View Answer A protein structural superfamily doesn’t have sequence-based PSI-BLAST profile

Which of the following is untrue about threading and fold recognition?


aIt assess the compatibility of an amino acid sequence with a known structure in a fold library

✖


bIf the protein fold to be predicted does not exist in the fold library, the method won’t necessarily fail

✓


cIf the protein fold to be predicted does not exist in the fold library, the method will fail

✖


dThreading and fold recognition do not generate fully refined atomic models for the query sequences

✖


View Answer If the protein fold to be predicted does not exist in the fold library, the method won’t necessarily fail

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


a without completely, far more sensitive

✓


bcompletely, far more sensitive

✖


ccompletely, less sensitive

✖


dwithout completely, less sensitive

✖


View Answer without completely, far more sensitive

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