SFP12: Protein Structure Prediction Flashcards
What protein database is manually annotated?
SwissProt
What protein database is automatically annotated?
TrEMBL
What is the BLAST in protein databases?
Identifying sequences similar to the query sequence (FASTA format)
What is FASTA?
Fast amino acid alignment
What is BLAST?
Basic logical alignment search tool
What is an alignment score?
Calculating the probability of finding a pair of AAs normalised to the probability of random occurrence (logarithm of): the higher the number, the better the alignment
When can residues be classed as similar?
If they are hydrophobic or negatively charged etc
If the structure of proteins with similar sequences are known what is used?
Template-based homologous modelling (TBM)
What are residues in sequence frequently found in helical elements?
Glu, Ala, leu, etc
Four out of six residues start a helix- continue in each direction until four helix -breakers, what are they?
Asparagine, tyrosine, proline and glycine
What amino acids does the formation of beta sheets require? (3 of them)
Methionine, valine, isoleucine, asparagine
What are the breakers of beta sheets?
Glutamine, histidine, lysine, serine, asparagine, proline
What residues are common with beta turns?
Glycine, proline, asparagine
What are the stages in homology modelling summarised?
- start with the linear sequence of the protein
- identify suitable templates
- choose homologous residues and atoms
- align segments
- fill gaps using first principles folding rules
- virtual translation
- minimise RMSD (root-mean-square deviation of atomic positions)
What is a target-based approach for identifying targets and ligands?
- identify candidate proteins from a genome
- structure based virtual screening (SBVS)
