Podcast Beta
Questions and Answers
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Which tool is used for sequence/alignment editing and has a file conversion feature for -fasta and -Nexus formats?
Which protein database is not mentioned in the text?
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
Signup and view all the answers
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
Signup and view all the answers
What are protein motifs usually associated with?
Signup and view all the answers
Where can information on protein families be found?
Signup and view all the answers
What reflects the evolution of complex proteins in many mammalian proteins?
Signup and view all the answers
Which tool can be used for protein secondary structure predictions?
Signup and view all the answers
What does the Protein Data Bank (PDB) contain?
Signup and view all the answers
What is the formula for Gibbs free energy?
Signup and view all the answers
What physiochemical property do nonpolar amino acid side chains exhibit?
Signup and view all the answers
What method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
Signup and view all the answers
Which atoms must buried polar atoms be bonded to, according to the considerations for protein folding?
Signup and view all the answers
What is the main purpose of excluding water molecules from the interior of a protein?
Signup and view all the answers
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
Signup and view all the answers
What resource can be used for searching the SWISS-MODEL template library for suitable template structures?
Signup and view all the answers
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
Signup and view all the answers
What method locates potential helical regions and beta strands in a protein sequence?
Signup and view all the answers
What is the main limitation of de novo prediction method for protein structure prediction?
Signup and view all the answers
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
Signup and view all the answers
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Signup and view all the answers
What is the formula for Gibbs free energy?
Signup and view all the answers
Which publication discusses Java bioinformatics analysis web services for multiple sequence alignment?
Signup and view all the answers
Where can information on protein families be found?
Signup and view all the answers
What is the main purpose of excluding water molecules from the interior of a protein?
Signup and view all the answers
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
Signup and view all the answers
Which method involves finding related proteins with known 3D structures to use as templates for modeling a protein's structure?
Signup and view all the answers
What reflects the evolution of complex proteins in many mammalian proteins?
Signup and view all the answers
Which tool is used for protein secondary structure predictions?
Signup and view all the answers
What method locates potential helical regions and beta strands in a protein sequence?
Signup and view all the answers
What are protein motifs usually associated with?
Signup and view all the answers
Which database can be used to scan a protein sequence for amino acid patterns known from previous work associated with a particular fold?
Signup and view all the answers
What is the main limitation of de novo prediction method for protein structure prediction?
Signup and view all the answers
Which program is described as a free program for multiple sequence alignment editing, visualization, and analysis?
Signup and view all the answers
Where can information on protein families be found?
Signup and view all the answers
What tool can be used to identify membrane-spanning proteins based on hydrophobicity?
Signup and view all the answers
What tool can be used to predict the secondary structure of proteins?
Signup and view all the answers
Where can information on protein domains be found?
Signup and view all the answers
What is the main purpose of the Protparam tool?
Signup and view all the answers
Which database contains three-dimensional structural data for proteins?
Signup and view all the answers
What reflects the evolution of complex proteins in many mammalian proteins?
Signup and view all the answers
Which tool can be used to identify membrane-spanning proteins based on hydrophobicity?
Signup and view all the answers
What physiochemical property do nonpolar amino acid side chains exhibit?
Signup and view all the answers
What does the PDB ID identify?
Signup and view all the answers
Which method involves scanning a protein sequence for amino acid patterns associated with particular folds?
Signup and view all the answers
What physiochemical property allows polar R groups to hydrogen bond with other polar groups or with polar solvents?
Signup and view all the answers
What reflects the evolution of complex proteins in many mammalian proteins?
Signup and view all the answers
Where can information on protein motifs be found?
Signup and view all the answers
Which tool can be used to study coevolution in protein families?
Signup and view all the answers
What is the purpose of Mutual Information Circos (MI Circo)?
Signup and view all the answers
What is the strategy involving Phyre2 and MISTIC?
Signup and view all the answers
What does the Colored square boxes of the second circle in Mutual Information Circos (MI Circo) indicate?
Signup and view all the answers
Which program is used for inter-protein contact prediction using deep learning?
Signup and view all the answers
What is the main purpose of the ConSurf server?
Signup and view all the answers
Which tool is used for protein dynamics and sequence analysis?
Signup and view all the answers
Where can information on the effect of mutations on protein structure be found?
Signup and view all the answers
What is the resource used for searching the SWISS-MODEL template library for suitable template structures?
Signup and view all the answers
What method does MEGA6 use for phylogenetic analysis?
Signup and view all the answers
Where can information on predicting the secondary structure of proteins be found?
Signup and view all the answers
What does the ConSurf server estimate based on phylogenetic relations between homologous sequences?
Signup and view all the answers
Which tool can be used to predict the effect of mutations on protein structure?
Signup and view all the answers
Where can information on estimating the evolutionary conservation of amino/nucleic acid positions be found?
Signup and view all the answers
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.
Studying That Suits You
Use AI to generate personalized quizzes and flashcards to suit your learning preferences.
Related Documents
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.