Homology modeling, also known as comparative modeling, is a computational technique used to predict the three-dimensional (3D) structure of a protein or other macromolecule based on its amino acid sequence and the known structure of a related protein or template. It involves aligning the sequence of the target protein with the template protein, transferring structural information from the template to the target, and generating a model that represents the likely 3D structure of the target protein. Homology modeling relies on the assumption that proteins with similar sequences share similar structures and functions. It is widely used in structural biology and drug discovery to gain insights into protein structure-function relationships, protein-ligand interactions, and protein-protein interactions.
Homology modeling is a computational technique used to:
a) Predict protein function
b) Determine protein sequence
c) Predict protein structure
d) Identify protein-protein interactions
Answer: c) Predict protein structure
The primary input required for homology modeling is:
a) Protein sequence
b) Protein structure
c) Protein function
d) Protein expression level
Answer: a) Protein sequence
The template used in homology modeling should have:
a) High sequence similarity to the target protein
b) Different fold compared to the target protein
c) No structural similarities with the target protein
d) Lower resolution than the target protein
Answer: a) High sequence similarity to the target protein
Which software tool is commonly used for homology modeling?
a) BLAST
b) PyMOL
c) MODELLER
d) SPSS
Answer: c) MODELLER
Homology modeling is less accurate when:
a) The target and template proteins have low sequence similarity
b) The target protein has a known structure
c) The template protein has a different fold than the target protein
d) The target protein has high expression levels
Answer: a) The target and template proteins have low sequence similarity
The process of modeling missing loop regions in homology modeling is called:
a) Template identification
b) Sequence alignment
c) Loop modeling
d) Model refinement
Answer: c) Loop modeling
The evaluation of homology models involves:
a) Assessing stereochemistry
b) Comparing with experimental data
c) Checking energy profiles
d) All of the above
Answer: d) All of the above
Homology modeling can be used to predict:
a) Protein sequence
b) Protein expression level
c) Protein-protein interactions
d) Protein function
Answer: d) Protein function
Which limitation is associated with homology modeling?
a) Inability to predict protein structure
b) High accuracy even with low sequence similarity
c) Dependence on experimental data
d) Difficulty in modeling loop regions
Answer: d) Difficulty in modeling loop regions
Which step in homology modeling involves transferring structural information from the template to the target protein?
a) Template identification
b) Sequence alignment
c) Model building
d) Model refinement
Answer: c) Model building
The accuracy of homology models depends on:
a) Sequence similarity between target and template proteins
b) Resolution of the template protein structure
c) Availability of experimental data
d) Length of the target protein sequence
Answer: a) Sequence similarity between target and template proteins
Homology modeling is commonly used in:
a) Drug discovery
b) DNA sequencing
c) Virus detection
d) Photosynthesis research
Answer: a) Drug discovery
Which software tool provides an automated homology modeling server?
a) SWISS-MODEL
b) PyMOL
c) MODELLER
d) I-TASSER
Answer: a) SWISS-MODEL
Homology modeling is a useful technique when experimental methods such as X-ray crystallography or NMR spectroscopy are:
a) Fast and cost-effective
b) Not feasible or time-consuming
c) Highly accurate and reliable
d) Only applicable to small proteins
Answer: b) Not feasible or time-consuming
The refinement of a homology model involves:
a) Energy minimization
b) Loop modeling
c) Comparative sequence analysis
d) Experimental validation
Answer: a) Energy minimization
