+1-315-636-4485
+91 98151-74050 
This quiz contains multiple-choice problems on protein secondary structure prediction, secondary structure and coiled-coil prediction.
The formation of __ is determined by __ interactions, whereas __ interactions strongly influence the formation of __.
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
The secondary structure prediction methods can be either ab initio based, which uses single sequence information only, or homology-based, which uses multiple sequence alignment information. True or false?
True
False
Which of the following is untrue regarding ab initio–based methods?
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 Chou–Fasman algorithm determines each residue's propensity or intrinsic tendency to be in the helix, strand, and β-turn conformation using observed frequencies found in protein crystal structures. True or false?
True
False
GOR method is based on the “propensity” of each residue to be in either the helix or strand conformational states. True or false?
True
False
Which of the following is incorrect regarding the Chou–Fasman and GOR methods?
Both are the first-generation methods
They were 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 incorrect regarding homology-based methods?
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 only the ab initio secondary structure prediction of individual sequences
This type of method combines the ab initio secondary structure prediction of individual sequences and alignment information from multiple homologous sequences (>35% identity)
Because residues in the same aligned position are assumed to have the same secondary structure, any inconsistencies or errors in the prediction of individual sequences can be corrected using a majority rule. True or false?
True
False
Which of the following is incorrect regarding prediction with neural networks?
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 regarding PHD?
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 the initial steps, it finds a set of homologous sequences which are aligned with the MAXHOM program (a weighted dynamic programming algorithm performing global alignment)
Coiled coils are superhelical structures involving two to more interacting α-helices from the same or different proteins. True or false?
True
False
Which of the following is true regarding coiled coil?
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 incorrect regarding 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
The scoring matrix is constructed in multi-coil based on a known three-stranded coiled coils database. True or false?
True
False
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. True or false?
True
False
