63 Questions
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Jalview
Which tool is used for sequence/alignment editing and has a file conversion feature for -fasta and -Nexus formats?
Jalview
Which protein database is not mentioned in the text?
KEGG
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
Procter JB et al. (2011)
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
ExPASY server (ProtScale)
What are protein motifs usually associated with?
Specific function
Where can information on protein families be found?
Pfam database
What reflects the evolution of complex proteins in many mammalian proteins?
'Mosaic proteins' due to domain shuffling
Which tool can be used for protein secondary structure predictions?
SWISS MODEL WORKSPACE
What does the Protein Data Bank (PDB) contain?
Three-dimensional structural data for proteins
What is the formula for Gibbs free energy?
G = H - TS
What physiochemical property do nonpolar amino acid side chains exhibit?
Hydrophobicity
What method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
Homology modeling
Which atoms must buried polar atoms be bonded to, according to the considerations for protein folding?
Other buried polar atoms
What is the main purpose of excluding water molecules from the interior of a protein?
To pack the interior densely
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
Fold recognition
What resource can be used for searching the SWISS-MODEL template library for suitable template structures?
SWISS-MODEL WORKSPACE Tools
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
Polarity
What method locates potential helical regions and beta strands in a protein sequence?
Attempts to predict secondary structures
What is the main limitation of de novo prediction method for protein structure prediction?
Difficulty in finding suitable templates for modeling
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
SWISS-MODEL
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Jalview
What is the formula for Gibbs free energy?
$ riangle G = riangle H - T riangle S$
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
Bioinformatics 27: 20012002
Where can information on protein families be found?
Pfam
What is the main purpose of excluding water molecules from the interior of a protein?
To densely pack the interior and stabilize the protein structure
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
Polarity
Which method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
Homology modeling
What reflects the evolution of complex proteins in many mammalian proteins?
Amino acid side chain physiochemical versatility
Which tool is used for protein secondary structure predictions?
$\text{Sequence Feature Scan}$
What method locates potential helical regions and beta strands in a protein sequence?
Attempts to predict secondary structures
What are protein motifs usually associated with?
Specific functions or activities
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
SWISS-MODEL Workspace
What is the main limitation of de novo prediction method for protein structure prediction?
It cannot predict novel folds.
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Expert Protein Analysis System (ExPASy)
Where can information on protein families be found?
NCBI resources
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
Sequence Feature Scan
What tool can be used to predict the secondary structure of proteins?
SWISS MODEL WORKSPACE
Where can information on protein domains be found?
Pfam database
What is the main purpose of the Protparam tool?
Obtaining basic information about a protein
Which database contains three-dimensional structural data for proteins?
Protein Data Bank (PDB)
What reflects the evolution of complex proteins in many mammalian proteins?
Mosaic proteins due to domain shuffling
Which tool can be used to identify membrane-spanning proteins based on hydrophobicity?
ProtScale
What physiochemical property do nonpolar amino acid side chains exhibit?
Low solubility in water
What does the PDB ID identify?
Three-dimensional structural data of proteins
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
Protein motifs identification using PROSITE library
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
Tendency to form hydrogen bonds with polar groups
What reflects the evolution of complex proteins in many mammalian proteins?
Mosaic proteins due to domain shuffling
Where can information on protein motifs be found?
PROSITE library
Which tool can be used to study coevolution in protein families?
MISTIC2
What is the purpose of Mutual Information Circos (MI Circo)?
To represent MSA position conservation and information content
What is the strategy involving Phyre2 and MISTIC?
Use Phyre2 to find nearest neighbors and use MISTIC to get preliminary secondary and 3D structure
What does the Colored square boxes of the second circle in Mutual Information Circos (MI Circo) indicate?
MSA position conservation
Which program is used for inter-protein contact prediction using deep learning?
ComplexContact
What is the main purpose of the ConSurf server?
Estimating the evolutionary conservation of amino/nucleic acid positions
Which tool is used for protein dynamics and sequence analysis?
ProDy
Where can information on the effect of mutations on protein structure be found?
foldxsuite.crg.eu
What is the resource used for searching the SWISS-MODEL template library for suitable template structures?
swissmodel.expasy.org/repository/
What method does MEGA6 use for phylogenetic analysis?
Maximum Likelihood (ML) method and Neighbor Joining (NJ) method plus bootstrap analysis
Where can information on predicting the secondary structure of proteins be found?
raptorx.uchicago.edu/ComplexContact/
What does the ConSurf server estimate based on phylogenetic relations between homologous sequences?
Evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule
Which tool can be used to predict the effect of mutations on protein structure?
foldxsuite.crg.eu
Where can information on estimating the evolutionary conservation of amino/nucleic acid positions be found?
Study Notes
Protein Structure and Function Overview
- Hydrophobicity can identify membrane-spanning proteins such as transporters or signal transducers, and ExPASY server (ProtScale) can be used for this purpose.
- ProtScale computes and represents the profile produced by any amino acid scale on a selected protein, based on different chemical and physical properties of the amino acids.
- Rps3 (ribosomal protein SSU #3) has hydrophobicity scores between 4.6 and -4.6, with a score of 4.6 being the most hydrophobic and a score of -4.6 being the most hydrophilic.
- A good start to get basic information about a protein, including hydrophobicity and other physiochemical properties, is the Protparam tool.
- Protein motifs are usually short conserved amino acid sequences associated with a specific function and can be found in the PROSITE library.
- Protein domains are regions of a protein that fold into semi-autonomous structures, and the Pfam database contains information on protein families.
- Many mammalian proteins are "Mosaic proteins" due to domain shuffling, which reflects the evolution of complex proteins.
- Protein secondary structure predictions can be made for helix, beta strands, coils, order/disorder using tools like SWISS MODEL WORKSPACE or PRALINE.
- The Protein Data Bank (PDB) is a database containing three-dimensional structural data for proteins.
- Protein stability and folding aim for the native state, which should be the thermodynamically most favorable state according to the second law of thermodynamics at constant temperature.
- The PDB ID is an accession number used to identify three-dimensional structural data of proteins.
- The Protein Secondary Structure Prediction Server can be used to predict the secondary structure of proteins.
Protein Structure and Function Overview
- Hydrophobicity can identify membrane-spanning proteins such as transporters or signal transducers, and ExPASY server (ProtScale) can be used for this purpose.
- ProtScale computes and represents the profile produced by any amino acid scale on a selected protein, based on different chemical and physical properties of the amino acids.
- Rps3 (ribosomal protein SSU #3) has hydrophobicity scores between 4.6 and -4.6, with a score of 4.6 being the most hydrophobic and a score of -4.6 being the most hydrophilic.
- A good start to get basic information about a protein, including hydrophobicity and other physiochemical properties, is the Protparam tool.
- Protein motifs are usually short conserved amino acid sequences associated with a specific function and can be found in the PROSITE library.
- Protein domains are regions of a protein that fold into semi-autonomous structures, and the Pfam database contains information on protein families.
- Many mammalian proteins are "Mosaic proteins" due to domain shuffling, which reflects the evolution of complex proteins.
- Protein secondary structure predictions can be made for helix, beta strands, coils, order/disorder using tools like SWISS MODEL WORKSPACE or PRALINE.
- The Protein Data Bank (PDB) is a database containing three-dimensional structural data for proteins.
- Protein stability and folding aim for the native state, which should be the thermodynamically most favorable state according to the second law of thermodynamics at constant temperature.
- The PDB ID is an accession number used to identify three-dimensional structural data of proteins.
- The Protein Secondary Structure Prediction Server can be used to predict the secondary structure of proteins.
This quiz covers topics related to proteins, protein databases such as UniProt and NCBI Protein, as well as sequence alignment tools like MAFFT and MUSCLE. It also includes information about the multiple sequence alignment editor Jalview.
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