Drug discovery 3&4 Flashcards
What is CASP?
Blind trial for testing structure prediction algorithms of determined structures before publication
How often is CASP performed?
Every two years
In energy minimisation is water a factor?
No
In Molecular dynamics is water a factor?
Yes
What are the limitations with energy minimisation?
Energy landscape not known hence difficult to identify lowest energy fold.
Also even if lowest energy minima found the protein may not exist in this structure
The accuracy of a 3 state prediction is known as what?
Q3
If secondary structures are assigned randomly what would the value Q3 to be?
33%
What was the function of Chou-Fausman?
To predict secondary structure
What is Chou-Fausman based on?
propensity of amino acid to exist in certain secondary structures. Each amino acid is given a score based on its propensity to exist in secondary structure
What is an average propensity of amino acids in Chou-Fausman?
1
1 < likely
1 > unlikely
What are the rules of Chou-Fausman?
A run out of 4 out of 6 residues favour helix then there will be a helix predicted.
Extend helix until a proline is reached or a run or 4 with propensity lower than 1
What is the principle of stereochemical method of secondary structure prediction developed by Lim?
Recognition of patterns of hydrophobic/hydrohpillic residues that favour secondary structures
Why is the stereochemical algorithm developed by lim empirical?
It is enhanced by inspection
What was the Q3 of the stereochemical algorithm developed by lim empirical?
60% - poor
What is an artificial neural networks?
Machine learning algorithm for assigning secondary structure after a training stage.
What was the Q3 of artifical neural network?
62%
How does MSA help with secondary structure prediction?
Highly conserved regions identifies important regions.
e.g. conserved sequence of aa of high alpha helix propensity is more likely to be an alpha helix
What was the Q3 when MSA is used?
77%
What is homology modelling?
Prediction a estruture based on a known structure of a similar protein
What is the first step of homology modelling?
Blast/PSI-blast
What follows the blast/psi-blast search in homology modelling?
Alignment of sequences of unknown with known (create MSA) - can be helpful to create alignment based on secondary structure prediction
What do you do if your MSA produced in homology modelling has gaps?
- Search for equivalent loops in PDB to fit the structure
- Energy minimisation of the loop
What type of loop is the best to predict?
Short loops (<6 residues), well predicted by all methods
After you substitute the sequence from known structure with the unknown structure and fit loops in what is the next step of homology modelling?
Pack side chains - given the backbone predict psi, phi, omega, chi
Only allowed angles need to be sampled
What are rotamer libraries?
Library of amino acid conformations - used for side chain packing in homology modelling
What is fold recognition (threading)?
Sequencing searching using secondary structure if no MSA can be found
What is a Hidden markov model
An algorithm that identifies distant homologues by matching secondary structure and sequence.
Give an examples of a programme that use HMM for protein structure prediction.
HHPRED
What is HHPRED?
A protein structure prediction algorithm based on homology modelling using a template found aligning sequence structure and amino acid sequence. Secondary structure prediction has to be manually inputted
Briefly what does Phyre do?
Run blast/psi-blast search, manual input of secondary structure, generation of HMM form MSA, use HHSearch to find template, Align, for backbone, loop modelling, side chain packing
What does phyrealarm do?
Checks programs very week for new hits as the database is constantly added to
What does Phyre investigator do?
Give information on which parts the prediction are reliable, what is functionally important and what residues are involved in protein interactions
What does the accuracy of a good template rely on?
A good MSA
When are ab initio methods required in protein structure prediction?
When no known templates are available
‘template free prediction’
What is an immunoglobulin fold?
Pair of stacked beta sheets running antiparallel with disulphide bonds in between
How many CDR classical structure (conical forms) are there?
2 - long and short
What does HAMA stand for?
Human Anti Mouse Antibody response
What is HAMA?
Mouse antibodies leading to an immune response in humans
What is a chimeric antibody?
Human except for the V domains
What is a full humanised antibody
Human except for the CDR domains
- steric clases exist between CDR and antibody so antibody has to be adapted an these changes are patented
What is Rosetta antibody?
Program for building 3D model for antibody
How does rosetta antibody work?
Take sequence of antibody
Homology model variable regions
Put together to create beta barrel
Graft on canoical loops
What is an antibody fragment?
The variable regions of the antibody. these can be used in isolation and linked with an artificial disulphide bond
Which CDR is hardest to model?
H3
