Which of the following is untrue about Loop Modeling Step?

The gaps cannot be directly modeled

In the sequence alignment for modeling, there are often regions caused by insertions and deletions producing gaps in sequence alignment

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

The gaps cannot be directly modeled

Loop modeling is required for closing the gaps requires

Which of the following is true regarding Prediction of β-Barrel Membrane Proteins?

For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are only hydrophilic in nature

For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are amphipathic in nature

For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are only hydrophilic in nature

For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are only hydrophobic in nature

They contain six to nine residues

Which of the following is untrue about homology modeling?

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 doesn’t involve the evolutionary distances anywhere

Which of the following is untrue about Ab initio prediction?

The perceived advantage of this method is that predictions are not restricted by known folds and that novel protein folds can be identified

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

Which of the following is untrue about SCOP and CATH?

The definition for class in CATH is quite dissimilar to that in SCOP

The definition for class in CATH is based on secondary structure content

Architecture is a unique level in CATH, intermediate between fold and class

The definition for class in CATH is similar to that in SCOP

Which of the following is wrong about Swiss-PDB Viewer?

It is essentially a Swiss-Army knife for structure visualization and modeling

It is a structure viewer for multiple platforms

It is a structure viewer for single platforms

It is essentially a Swiss-Army knife for structure visualization and modeling

It is capable of structure visualization, analysis, and homology modeling

Which of the following is incorrect about intermolecular approach?

This procedure starts with identifying equivalent residues or atoms

After residue–residue correspondence is established, one of the structures is moved laterally and vertically toward the other structure to allow the two structures to be in the same location

The structures are rotated relative to each other around the three-dimensional axes

The rotation doesn’t depend on the intermolecular distance

Which of the following is not correct about the NMR?

NMR spectroscopy detects spinning patterns of atomic nuclei in a magnetic field

It stands for Nuclear Magnetic Resonance

NMR spectroscopy detects spinning patterns of atomic nuclei in a electric field

NMR spectroscopy detects spinning patterns of atomic nuclei in a magnetic field

Protein samples are labeled with radioisotopes such as 13C and 15N

Which of the following is not correct about the Integral Membrane Proteins?

Most typical transmembrane segments are α-helices

Membrane proteins exist in lipid bilayers of cell membranes

The exterior of the proteins spanning the membrane must be very hydrophobic to be stable

The exterior of the proteins spanning the membrane must be very hydrophilic to be stable

Most typical transmembrane segments are α-helices

Which of the following is not correct about the β-sheet?

β-Strands are stabilized by hydrogen bonds between residues of adjacent strands

A β-sheet is a fully extended configuration built up from several spatially adjacent regions of a polypeptide chain

Each region involved in forming the β-sheet is a β-strand

The β-strand conformation is pleated with main chain backbone zigzagging and side chains positioned on same sides of the sheet

β-Strands are stabilized by hydrogen bonds between residues of adjacent strands

Which of the following is not correct about the α-Helices?

Nearly all known α-helices are right handed, exhibiting a rightward spiral form

An α-helix has a main chain backbone conformation that resembles a corkscrew

Nearly all known α-helices are right handed, exhibiting a leftward spiral form

Nearly all known α-helices are right handed, exhibiting a rightward spiral form

In right handed helix, there are 3.6 amino acids per helical turn

Which of the following is not correct?

A peptide bond is actually a partial double bond owing to shared electrons between O=C–N atoms

The rigid double bond structure forces atoms associated with the peptide bond to lie in the same plane, called the dipeptide plane

A peptide bond is actually a partial double bond owing to shared electrons between O=C–N atoms

Because of the planar nature of the peptide bond and the size of the R groups, there are considerable restrictions on the rotational freedom by the two bonded pairs of atoms around the peptide bond

The angle of rotation about the bond is referred to as the dihedral angle (also called the torsional angle)

Which of the following is not correct about the X-ray Crystallography?

In x-ray protein crystallography, proteins need to be grown into large crystals in which their positions are fixed in a repeated, ordered fashion

The protein crystals are illuminated with an intense x-ray beam

The x-rays are deflected by the electron clouds surrounding the atoms in the crystal producing a regular pattern of diffraction

The protein crystals are illuminated with an intense infrared beam

Which of the following is untrue regarding Prediction with Neural Networks?

A neural network is trained by a sequence profile derived from the multiple sequence alignment

When multiple sequence alignments and neural networks are combined, the result is further improved accuracy

A neural network is trained by a single sequence

A neural network is trained by a sequence profile derived from the multiple sequence alignment

When the sufficiently trained network processes an unknown sequence, it applies the rules learned in training to recognize particular structural patterns

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

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

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

Which of the following is true regarding Coiled coil?

They have an integral repeat of thirty residues

They have an integral repeat of twenty residues

They have an integral repeat of seven residues

They have an integral repeat of thirty residues

The sequence periodicity doesn’t contribute in designing algorithms to predict the structural domain.

Which of the following is untrue regarding the transmembrane proteins?

Constitute up to 30% of all cellular proteins

They are responsible for performing a wide variety of important functions in a cell, such as signal transduction, cross-membrane transport, and energy conversion

The membrane proteins are also of tremendous biomedical importance

They are not drug targets or receptors

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

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

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 not correct about the stabilizing Forces?

Electrostatic interactions are a significant stabilizing force in a protein structure

Protein structures from secondary to quaternary are maintained by noncovalent forces

They include electrostatic interactions but not van der Waals forces, and hydrogen bonding

Electrostatic interactions are a significant stabilizing force in a protein structure

Electrostatic interactions occur when excess negative charges in one region are neutralized by positive charges in another region

Which of the following is an incorrect statement?

Chime is a plug-in for web browsers

WebMol is a web-based program built based on a modified RasMol code and thus shares many similarities with RasMol

WebMol is a web-based program that is totally different from RasMol

Chime is a plug-in for web browsers

Chime is not a standalone program and has to be invoked in a web browser

Which of the following is incorrect about SSAP?

Dynamic programming approach is used

It is a web server that uses an intramolecular distance–based method

Matrices are built based on the Cβ distances of all residue pairs

Dynamic programming approach is not used here

Dynamic programming approach is used

Which of the following is untrue regarding Prediction with Neural Networks?

It requires a structure of multiple layers of interconnected variables or nodes

The third-generation prediction algorithms extensively apply sophisticated neural networks

It is used to analyze substitution patterns in multiple sequence alignments

It is not a machine learning process

It requires a structure of multiple layers of interconnected variables or nodes

Which of the following is incorrect about the intramolecular approach?

In comparing two protein structures, the distance matrices from the two structures are moved relative to each other to achieve maximum overlaps

The method works by generating a distance matrix between residues of the same protein

It generates a string between residues of the same protein

In comparing two protein structures, the distance matrices from the two structures are moved relative to each other to achieve maximum overlaps

By overlaying two distance matrices, similar intramolecular distance patterns representing similar structure folding regions can be identified

Which of the following is untrue about SCOP?

It is a database for comparing and classifying protein structures

It is constructed almost entirely based on manual examination of protein structures

The proteins are grouped into hierarchies of classes, folds, superfamilies, and families

The SCOP families consist of proteins having low sequence identity (>30%)

98 + Mcqs in Structural Bioinformatics in Bioinformatics Page 1 McqOptions

1.	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 requires
Answer» C. The gaps cannot be directly modeled

3.	The algorithms used here can be classified into two categories, pairwise energy based and profile based.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

4.	Energy minimization has to be used with caution because excessive energy minimization often moves residues away from their correct positions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

6.	Coiled coils are super helical structures involving two to more interacting α-helices from the same or different proteins.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

8.	The early algorithms based their prediction on hydrophobicity scales.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

9.	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.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

10.	The structures of this group of proteins, however, are comparatively a lot difficult to resolve either by x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

11.	Searching for a fold with the absolute minimum energy may not be valid in reality.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

13.	The first step in structure classification is to remove redundancy from databases.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

14.	Members within the ____ fold ______ have evolutionary relationships.
A.	same, always
B.	same, do not always
C.	one, always
D.	different, do not
Answer» C. one, always

15.	The last step in structure classification involves grouping proteins/domains of similar structures.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

36.	Ribbon diagrams use cylinders or spiral ribbons to represent α-helices and broad, flat arrows to represent β-strands.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

16.	VAST is a web server that performs alignment using intramolecular approaches only.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

17.	Ribbons another UNIX program similar to Molscript, generates ribbon diagrams depicting protein secondary structures.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

20.	A wire-frame diagram is a line drawing representing bonds between atoms.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

21.	Balls and sticks are solid spheres and rods, representing atoms and bonds, respectively.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

22.	A Protein Data Bank (PDB) data file for a protein structure contains only x, and z coordinates of atoms.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

24.	The next step in the pairwise energy based method is to build a crude model for the target sequence by replacing aligned residues in the template structure with the corresponding residues in the query.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

29.	The Chou–Fasman algorithm determines the propensity or intrinsic tendency of each residue to be in the helix, strand, and β-turn conformation using observed frequencies found in protein crystal structures.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

30.	The intermolecular approach is normally applied to relatively _____ structures.
A.	distinctive
B.	dissimilar
C.	similar
D.	different
Answer» D. different

31.	There are a large number of protein folds available, compared to millions of protein sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

34.	The intramolecular approach does not depend on sequence similarity between the proteins to be compared.
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 about Loop Modeling Step?

Which of the following is true regarding Prediction of β-Barrel Membrane Proteins?

The algorithms used here can be classified into two categories, pairwise energy based and profile based.

Energy minimization has to be used with caution because excessive energy minimization often moves residues away from their correct positions.

Which of the following is untrue about homology modeling?

Coiled coils are super helical structures involving two to more interacting α-helices from the same or different proteins.

Which of the following is untrue about Ab initio prediction?

The early algorithms based their prediction on hydrophobicity scales.

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.

The structures of this group of proteins, however, are comparatively a lot difficult to resolve either by x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy.

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

Which of the following is untrue about SCOP and CATH?

The first step in structure classification is to remove redundancy from databases.

Members within the ____ fold ______ have evolutionary relationships.

The last step in structure classification involves grouping proteins/domains of similar structures.

VAST is a web server that performs alignment using intramolecular approaches only.

Ribbons another UNIX program similar to Molscript, generates ribbon diagrams depicting protein secondary structures.

Which of the following is wrong about Swiss-PDB Viewer?

Which of the following is incorrect about intermolecular approach?

A wire-frame diagram is a line drawing representing bonds between atoms.

Balls and sticks are solid spheres and rods, representing atoms and bonds, respectively.

A Protein Data Bank (PDB) data file for a protein structure contains only x, and z coordinates of atoms.

Which of the following is not correct about the NMR?

The next step in the pairwise energy based method is to build a crude model for the target sequence by replacing aligned residues in the template structure with the corresponding residues in the query.

Which of the following is not correct about the Integral Membrane Proteins?

Which of the following is not correct about the β-sheet?

Which of the following is not correct about the α-Helices?

Which of the following is not correct?

The Chou–Fasman algorithm determines the propensity or intrinsic tendency of each residue to be in the helix, strand, and β-turn conformation using observed frequencies found in protein crystal structures.

The intermolecular approach is normally applied to relatively _____ structures.

There are a large number of protein folds available, compared to millions of protein sequences.

Which of the following is not correct about the X-ray Crystallography?

Which of the following is untrue regarding Prediction with Neural Networks?

The intramolecular approach does not depend on sequence similarity between the proteins to be compared.

Jpred combines the analysis results from six prediction algorithms, including PHD, PREDATOR, DSC, NNSSP, Jnet, and ZPred.

Ribbon diagrams use cylinders or spiral ribbons to represent α-helices and broad, flat arrows to represent β-strands.

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

Which of the following is true regarding Coiled coil?

Which of the following is untrue regarding the transmembrane proteins?

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

Which of the following is not correct about the stabilizing Forces?

Which of the following is an incorrect statement?

Which of the following is incorrect about SSAP?

SCOP is _______ based on manual comparison of structures by human experts with no quantitative criteria to group proteins.

Different representation styles can be used in combination to highlight a certain feature of a structure while deemphasizing the structures surrounding it.

Which of the following is untrue regarding Prediction with Neural Networks?

Which of the following is incorrect about the intramolecular approach?

Because residues in the same aligned position are assumed to have the same secondary structure, any inconsistencies or errors in prediction of individual sequences can be corrected using a majority rule.

Which of the following is untrue about SCOP?

Predictions solely based on hydrophobicity profiles have lowest error rates.

Members within the fold __ have evolutionary relationships.

44.	SCOP is _______ based on manual comparison of structures by human experts with no quantitative criteria to group proteins.
A.	entirely
B.	almost entirely
C.	not
D.	partially
Answer» C. not