Podcast
Questions and Answers
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
- Jalview (correct)
- InterPro
- UniProt
- NCBI Protein
Which tool is used for sequence/alignment editing and has a file conversion feature for -fasta and -Nexus formats?
Which tool is used for sequence/alignment editing and has a file conversion feature for -fasta and -Nexus formats?
- Pfam
- MUSCLE
- Jalview (correct)
- MAFFT
Which protein database is not mentioned in the text?
Which protein database is not mentioned in the text?
- PDB
- KEGG (correct)
- UniProt
- GenBank
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
What are protein motifs usually associated with?
What are protein motifs usually associated with?
Where can information on protein families be found?
Where can information on protein families be found?
What reflects the evolution of complex proteins in many mammalian proteins?
What reflects the evolution of complex proteins in many mammalian proteins?
Which tool can be used for protein secondary structure predictions?
Which tool can be used for protein secondary structure predictions?
What does the Protein Data Bank (PDB) contain?
What does the Protein Data Bank (PDB) contain?
What is the formula for Gibbs free energy?
What is the formula for Gibbs free energy?
What physiochemical property do nonpolar amino acid side chains exhibit?
What physiochemical property do nonpolar amino acid side chains exhibit?
What method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
What method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
Which atoms must buried polar atoms be bonded to, according to the considerations for protein folding?
Which atoms must buried polar atoms be bonded to, according to the considerations for protein folding?
What is the main purpose of excluding water molecules from the interior of a protein?
What is the main purpose of excluding water molecules from the interior of a protein?
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
What resource can be used for searching the SWISS-MODEL template library for suitable template structures?
What resource can be used for searching the SWISS-MODEL template library for suitable template structures?
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
What method locates potential helical regions and beta strands in a protein sequence?
What method locates potential helical regions and beta strands in a protein sequence?
What is the main limitation of de novo prediction method for protein structure prediction?
What is the main limitation of de novo prediction method for protein structure prediction?
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
What is the formula for Gibbs free energy?
What is the formula for Gibbs free energy?
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
Where can information on protein families be found?
Where can information on protein families be found?
What is the main purpose of excluding water molecules from the interior of a protein?
What is the main purpose of excluding water molecules from the interior of a protein?
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
Which method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
Which method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
What reflects the evolution of complex proteins in many mammalian proteins?
What reflects the evolution of complex proteins in many mammalian proteins?
Which tool is used for protein secondary structure predictions?
Which tool is used for protein secondary structure predictions?
What method locates potential helical regions and beta strands in a protein sequence?
What method locates potential helical regions and beta strands in a protein sequence?
What are protein motifs usually associated with?
What are protein motifs usually associated with?
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
What is the main limitation of de novo prediction method for protein structure prediction?
What is the main limitation of de novo prediction method for protein structure prediction?
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Where can information on protein families be found?
Where can information on protein families be found?
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
What tool can be used to predict the secondary structure of proteins?
What tool can be used to predict the secondary structure of proteins?
Where can information on protein domains be found?
Where can information on protein domains be found?
What is the main purpose of the Protparam tool?
What is the main purpose of the Protparam tool?
Which database contains three-dimensional structural data for proteins?
Which database contains three-dimensional structural data for proteins?
What reflects the evolution of complex proteins in many mammalian proteins?
What reflects the evolution of complex proteins in many mammalian proteins?
Which tool can be used to identify membrane-spanning proteins based on hydrophobicity?
Which tool can be used to identify membrane-spanning proteins based on hydrophobicity?
What physiochemical property do nonpolar amino acid side chains exhibit?
What physiochemical property do nonpolar amino acid side chains exhibit?
What does the PDB ID identify?
What does the PDB ID identify?
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
What reflects the evolution of complex proteins in many mammalian proteins?
What reflects the evolution of complex proteins in many mammalian proteins?
Where can information on protein motifs be found?
Where can information on protein motifs be found?
Which tool can be used to study coevolution in protein families?
Which tool can be used to study coevolution in protein families?
What is the purpose of Mutual Information Circos (MI Circo)?
What is the purpose of Mutual Information Circos (MI Circo)?
What is the strategy involving Phyre2 and MISTIC?
What is the strategy involving Phyre2 and MISTIC?
What does the Colored square boxes of the second circle in Mutual Information Circos (MI Circo) indicate?
What does the Colored square boxes of the second circle in Mutual Information Circos (MI Circo) indicate?
Which program is used for inter-protein contact prediction using deep learning?
Which program is used for inter-protein contact prediction using deep learning?
What is the main purpose of the ConSurf server?
What is the main purpose of the ConSurf server?
Which tool is used for protein dynamics and sequence analysis?
Which tool is used for protein dynamics and sequence analysis?
Where can information on the effect of mutations on protein structure be found?
Where can information on the effect of mutations on protein structure be found?
What is the resource used for searching the SWISS-MODEL template library for suitable template structures?
What is the resource used for searching the SWISS-MODEL template library for suitable template structures?
What method does MEGA6 use for phylogenetic analysis?
What method does MEGA6 use for phylogenetic analysis?
Where can information on predicting the secondary structure of proteins be found?
Where can information on predicting the secondary structure of proteins be found?
What does the ConSurf server estimate based on phylogenetic relations between homologous sequences?
What does the ConSurf server estimate based on phylogenetic relations between homologous sequences?
Which tool can be used to predict the effect of mutations on protein structure?
Which tool can be used to predict the effect of mutations on protein structure?
Where can information on estimating the evolutionary conservation of amino/nucleic acid positions be found?
Where can information on estimating the evolutionary conservation of amino/nucleic acid positions be found?
Flashcards
Membrane-spanning proteins
Membrane-spanning proteins
Proteins that span biological membranes, often involved in transport or signaling.
ProtScale
ProtScale
ExPASy server tool to analyze protein hydrophobicity.
Hydrophobicity
Hydrophobicity
The tendency of a molecule to repel water.
ProtParam
ProtParam
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Protein Motifs
Protein Motifs
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PROSITE
PROSITE
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Protein Domains
Protein Domains
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Pfam
Pfam
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Mosaic proteins
Mosaic proteins
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Domain shuffling
Domain shuffling
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Protein secondary structure
Protein secondary structure
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SWISS MODEL WORKSPACE
SWISS MODEL WORKSPACE
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PRALINE
PRALINE
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PDB
PDB
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PDB ID
PDB ID
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Protein Stability
Protein Stability
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Native State
Native State
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Protein Folding
Protein Folding
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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.
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Description
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.
