Which of the following is untrue regarding Prediction of Helical Membrane Proteins?

The α-helices have an average length between seventeen and twenty-five residues

For membrane proteins consisting of transmembrane α–helices, these transmembrane helices are predominantly hydrophobic with a specific distribution of positively charged residues

The α-helices generally run perpendicular to the membrane plane

The α-helices generally run parallel to the membrane plane

The α-helices have an average length between seventeen and twenty-five residues

Which of the following is untrue regarding Coils?

It compares the sequence to a probability matrix compiled from known parallel two-stranded coiled coils

It is a web-based program that detects coiled coil regions in proteins

It scans a window of fourteen, twenty-one, or twenty-eight residues

It scans a window of fourteen or twenty-one residues only

It compares the sequence to a probability matrix compiled from known parallel two-stranded coiled coils

Which of the following is untrue regarding Homology-Based Methods?

This type of method combines the ab initio secondary structure prediction of individual sequences and alignment information from multiple homologous sequences (>35% identity)

The third generation of algorithms was developed in the late 1990s

They were developed by making use of evolutionary information

This type of method uses the ab initio secondary structure prediction of individual sequences only

This type of method combines the ab initio secondary structure prediction of individual sequences and alignment information from multiple homologous sequences (>35% identity)

The root mean square deviation (RMSD), without the size dependency correction is?

\(\sum_{i=1}^N \frac{D_i^2}{N + 1}\)

\(\sum_{i=1}^N \frac{D_i^2}{N}\)

\(\sum_{i=1}^N \frac{D_i^2}{N + 1}\)

\(\sum_{i=1}^N \frac{D_i^2}{N x N}\)

\(\sum_{i=1}^N \frac{D_i^2}{N – 1}\)

Which of the following is untrue about 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 untrue regarding PHD?

It first performs a BLASTP of the query sequence against a non redundant protein sequence database

It stands for Profile network from Heidelberg

It is a web-based program that combines neural network only

It first performs a BLASTP of the query sequence against a non redundant protein sequence database

In initial steps it finds a set of homologous sequences, which are aligned with the MAXHOM program (a weighted dynamic programming algorithm performing global alignment)

Which of the following is incorrect about Multiple Structure Alignment?

All structures are first compared in a pairwise fashion

The alignment strategy is different than the Clustal sequence alignment using a progressive approach

All structures are first compared in a pairwise fashion

A distance matrix is developed based on structure similarity scores such as RMSD

The aligned structures create a median structure that allows other structures to be progressively added for comparison based on the hierarchy described in the guide tree

The root mean square deviation (RMSD), with the size dependency correction is?

\(\frac{RMSD}{-1.3 + 0.5 ln⁡(N+1)}\)

\(\frac{RMSD}{-1.3 + 0.5 ln⁡(N x N)}\)

\(\frac{RMSD}{-1.3 + 0.5 ln⁡(N-1)}\)

\(\frac{RMSD}{-1.3 + 0.5 ln⁡(N)}\)

Which of the following is not correct about the Coils and Loops?

The loops are often characterized by sharp turns or hairpin-like structures

If the connecting regions are completely irregular, they belong to random coils

Which of the following is untrue regarding PSIPRED?

The multiple sequence alignment is derived from a PSI-BLAST database search

It is a web-based program that predicts protein secondary structures

It uses a combination of evolutionary information and neural networks

It uses a combination of evolutionary information only

The multiple sequence alignment is derived from a PSI-BLAST database search

Which of the following is untrue regarding Chou–Fasman and GOR methods?

Both are the first-generation methods

They are developed in the 1970s

They suffer from the fact that the prediction rules are somewhat arbitrary

They are based on single sequence statistics with clear relation to known protein-folding theories

Which of the following is untrue regarding Ab Initio–Based Methods?

It measures the relative propensity of each amino acid belonging to a certain secondary structure element

This type of method predicts the secondary structure based on a single query sequence

This type of method predicts the secondary structure based on a multiple query sequence

It measures the relative propensity of each amino acid belonging to a certain secondary structure element

The propensity scores are derived from known crystal structures

The formation of _____ is determined by ______ interactions, whereas the formation of ____ is strongly influenced by ______ interactions.

β-strands, short-range, β-strands, long-range

α-helices, long-range, α-helices, short-range

α-helices, long-range, β-strands, short-range

α-helices, short-range, β-strands, long-range

β-strands, short-range, β-strands, long-range

Which of the following is incorrect about protein structure comparison?

Proteins can share common structures even without sequence similarity

The comparative approach is important in finding remote protein homologs

Protein structures have a much higher degree of conservation than the sequences

Protein structures have a much lesser degree of conservation than the sequences

Proteins can share common structures even without sequence similarity

Which of the following is untrue about template Selection Step?

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

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 untrue regarding Phobius?

The program incorporates distinct HMM models for signal peptides as well as transmembrane helices

It is a web-based program designed to overcome false positives caused by the presence of signal peptides

The program incorporates distinct HMM models for signal peptides only

The program incorporates distinct HMM models for signal peptides as well as transmembrane helices

After distinguishing the putative signal peptides from the rest of the query sequence, prediction is made on the remainder of the sequence

Which of the following is untrue regarding TMHMM?

When a query sequence is scanned, the probability of having an α-helical domain is given

It is a web-based program based on an HMM algorithm

It is trained to recognize transmembrane helical patterns

It is not trained to recognize transmembrane helical patterns

When a query sequence is scanned, the probability of having an α-helical domain is given

In CATH, Structural domain separation is carried by ___________

a combined effort of a human expert and computer programs

Which of the following is untrue about profile method?

Statistical information from these aligned residues is then used to construct a profile

A profile is constructed for a group of related protein structures

The propensity of amino acids in not in picture of this method

Statistical information from these aligned residues is then used to construct a profile

The structural profile is generated by the superimposition of the structures to expose corresponding residues

Which of the following is untrue about 3D-PSSM?

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

It is a web-based program that employs the structural profile method to identify protein folds

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

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

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

Which of the following is true about Gen Threader?

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

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

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

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

The initial step is quite dissimilar to 3D-PSSM

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

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

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

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

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

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

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

without completely, far more sensitive

without completely, less sensitive

98 + Mcqs in Structural Bioinformatics in Bioinformatics Page 2 McqOptions

51.	Which of the following is untrue regarding Prediction of Helical Membrane Proteins?
A.	For membrane proteins consisting of transmembrane α–helices, these transmembrane helices are predominantly hydrophobic with a specific distribution of positively charged residues
B.	The α-helices generally run perpendicular to the membrane plane
C.	The α-helices generally run parallel to the membrane plane
D.	The α-helices have an average length between seventeen and twenty-five residues
Answer» D. The α-helices have an average length between seventeen and twenty-five residues

53.	Prof is not similar to PHD.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

56.	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.	False
C.	May be True or False
D.	Can't say
Answer» B. False

57.	Leucine zipper domains are a special type of coiled coils found in transcription regulatory proteins which contain two anti parallel α-helices held together by hydrophobic interactions of leucine residues.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

58.	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.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

59.	In Rosetta, The segments with assigned _______ structures are subsequently assembled into a ______ dimensional configuration.
A.	primary, three
B.	secondary, three
C.	secondary, two
D.	primary, three
Answer» C. secondary, two

61.	Rosetta is a web server that predicts protein three-dimensional conformations using the ab initio method.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

62.	The main feature of computer visualization programs is interactivity, which allows users to visually manipulate the structural images through a graphical user interface.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

63.	The classification results from both systems, SCOP and CATH are quite dissimilar.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

64.	The secondary structure prediction methods can be either ab initio based, which make use of single sequence information only, or homology based, which makes use of multiple sequence alignment information.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

66.	Scanning a sequence by hydrophobicity does not reveal transmembrane β-strands.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

71.	The presence of ______ signal peptides can significantly compromise the prediction _______ because the programs tend to confuse hydrophobic signal peptides with membrane helices.
A.	hydrophobic, accuracy
B.	hydrophobic, error
C.	hydrophilic, accuracy
D.	hydrophilic, error
Answer» B. hydrophobic, error

67.	CATH is a combination of manual curation and automated procedure, which makes the process less subjective.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

70.	Which of the following is not correct about the Coils and Loops?
A.	They are regular structures
B.	They are irregular structures
C.	The loops are often characterized by sharp turns or hairpin-like structures
D.	If the connecting regions are completely irregular, they belong to random coils
Answer» B. They are irregular structures

72.	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.	False
C.	May be True or False
D.	Can't say
Answer» B. False

75.	The GOR method is based on the “propensity” of each residue to be in one of the two conformational states, helix (H), strand(E).
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

76.	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-based
Answer» D. residue-based

77.	In Multicoil, The scoring matrix is constructed based on a database of known three-stranded coiled coils only.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

78.	The second step in structure classification is to separate structurally distinct domains within a structure.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

80.	One can search a structure in PDB using the four-letter code or keywords related to its annotation.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

84.	Globular proteins are usually insoluble.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

87.	The prediction programs are thus designed using the energy minimization principle.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

Which of the following is untrue regarding Prediction of Helical Membrane Proteins?

Which of the following is untrue regarding Coils?

Prof is not similar to PHD.

Which of the following is untrue regarding Homology-Based Methods?

The root mean square deviation (RMSD), without the size dependency correction is?

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.

Leucine zipper domains are a special type of coiled coils found in transcription regulatory proteins which contain two anti parallel α-helices held together by hydrophobic interactions of leucine residues.

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.

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

Which of the following is untrue about Sequence Alignment Step?

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

The main feature of computer visualization programs is interactivity, which allows users to visually manipulate the structural images through a graphical user interface.

The classification results from both systems, SCOP and CATH are quite dissimilar.

The secondary structure prediction methods can be either ab initio based, which make use of single sequence information only, or homology based, which makes use of multiple sequence alignment information.

Which of the following is untrue regarding PHD?

Scanning a sequence by hydrophobicity does not reveal transmembrane β-strands.

CATH is a combination of manual curation and automated procedure, which makes the process less subjective.

Which of the following is incorrect about Multiple Structure Alignment?

The root mean square deviation (RMSD), with the size dependency correction is?

Which of the following is not correct about the Coils and Loops?

The presence of ______ signal peptides can significantly compromise the prediction _______ because the programs tend to confuse hydrophobic signal peptides with membrane helices.

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.

Which of the following is untrue regarding PSIPRED?

Which of the following is untrue regarding Chou–Fasman and GOR methods?

The GOR method is based on the “propensity” of each residue to be in one of the two conformational states, helix (H), strand(E).

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.

In Multicoil, The scoring matrix is constructed based on a database of known three-stranded coiled coils only.

The second step in structure classification is to separate structurally distinct domains within a structure.

Which of the following is untrue regarding Ab Initio–Based Methods?

One can search a structure in PDB using the four-letter code or keywords related to its annotation.

The formation of _____ is determined by ______ interactions, whereas the formation of ____ is strongly influenced by ______ interactions.

Which of the following is incorrect about protein structure comparison?

Which of the following is untrue about template Selection Step?

Globular proteins are usually insoluble.

Which of the following is untrue regarding Phobius?

Which of the following is untrue regarding TMHMM?

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

In CATH, Structural domain separation is carried by ___________

Which of the following is untrue about profile method?

Which of the following is untrue about 3D-PSSM?

Which of the following is true about Gen Threader?

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

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

The peptide formation involves two amino acids covalently joined together between the carboxyl group of one amino acid and the amino group of another.

A linear polymer of more than fifty amino acid residues is referred to as a ________

______ the smallest amino acid, has a hydrogen atom as the R group.

Within the hydrophobic set of amino acids, they can be further divided into aliphatic and aromatic.

The building blocks of proteins are ______ naturally occurring amino acids, small molecules that contain a free amino group (NH₂) and a free carboxyl group (COOH).

In Rosetta, The segments with assigned _ structures are subsequently assembled into a dimensional configuration.

The presence of signal peptides can significantly compromise the prediction _ because the programs tend to confuse hydrophobic signal peptides with membrane helices.

The formation of _ is determined by interactions, whereas the formation of is strongly influenced by ____ interactions.

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

88.	In CATH, Structural domain separation is carried by ___________
A.	manual comparison only
B.	computer programs only
C.	human expertise only
D.	a combined effort of a human expert and computer programs
Answer» E.

93.	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
B.	completely, far more sensitive
C.	completely, less sensitive
D.	without completely, less sensitive
Answer» B. completely, far more sensitive

95.	A linear polymer of more than fifty amino acid residues is referred to as a ________
A.	dipeptide
B.	oligopeptide
C.	peptide
D.	polypeptide
Answer» E.

96.	______ the smallest amino acid, has a hydrogen atom as the R group.
A.	valine
B.	proline
C.	Glycine
D.	threonine
Answer» D. threonine

98.	The building blocks of proteins are ______ naturally occurring amino acids, small molecules that contain a free amino group (NH₂) and a free carboxyl group (COOH).
A.	ten
B.	twenty
C.	nine
D.	nineteen
Answer» C. nine