Sequence Structure Flashcards
What is a hydrogen bond?
Formed when a proton covalently attached to one electronegative donor shared with another electronegative acceptor.
How were propensities calculated?
In 1974 less than 2500 residues to accurately determine values.
By 2004 structure data sets large enough to derive residue propensities at different positions within alpha helices.
In 1999 A Janet Thornton determined beta turn propensities based on over 4000 beta turns.
What is accuracy?
True positives + true negatives / positives + negatives.
What is tertiary structure?
No and order of SS in sequence and their ARRANGEMENT in space .
What are the two models of protein folding ?
Diffusion collision - SS elements form first and then collide with other SS elements (favoured by alpha helical proteins)
Nucleation condensation - general compaction then nucleation of native secondary and tertiary structure (favoured by beta sheet proteins).
What are the methods of structural prediction?
Simulation based
Knowledge-based scoring functions (above are ab-initio)
Template based.
How is threading assessed?
Goodness of fit score derived in terms of empiracle energy function based on statistics derived from known protein structures.
