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Biotechnology > Drug discovery 3&4 > Flashcards

Drug discovery 3&4 Flashcards

1
Q

What is CASP?

A

Blind trial for testing structure prediction algorithms of determined structures before publication

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2
Q

How often is CASP performed?

A

Every two years

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3
Q

In energy minimisation is water a factor?

A

No

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4
Q

In Molecular dynamics is water a factor?

A

Yes

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5
Q

What are the limitations with energy minimisation?

A

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

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6
Q

The accuracy of a 3 state prediction is known as what?

A

Q3

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7
Q

If secondary structures are assigned randomly what would the value Q3 to be?

A

33%

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8
Q

What was the function of Chou-Fausman?

A

To predict secondary structure

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9
Q

What is Chou-Fausman based on?

A

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

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10
Q

What is an average propensity of amino acids in Chou-Fausman?

A

1
1 < likely
1 > unlikely

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11
Q

What are the rules of Chou-Fausman?

A

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

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12
Q

What is the principle of stereochemical method of secondary structure prediction developed by Lim?

A

Recognition of patterns of hydrophobic/hydrohpillic residues that favour secondary structures

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13
Q

Why is the stereochemical algorithm developed by lim empirical?

A

It is enhanced by inspection

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14
Q

What was the Q3 of the stereochemical algorithm developed by lim empirical?

A

60% - poor

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15
Q

What is an artificial neural networks?

A

Machine learning algorithm for assigning secondary structure after a training stage.

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16
Q

What was the Q3 of artifical neural network?

A

62%

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17
Q

How does MSA help with secondary structure prediction?

A

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

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18
Q

What was the Q3 when MSA is used?

A

77%

19
Q

What is homology modelling?

A

Prediction a estruture based on a known structure of a similar protein

20
Q

What is the first step of homology modelling?

A

Blast/PSI-blast

21
Q

What follows the blast/psi-blast search in homology modelling?

A

Alignment of sequences of unknown with known (create MSA) - can be helpful to create alignment based on secondary structure prediction

22
Q

What do you do if your MSA produced in homology modelling has gaps?

A
  • Search for equivalent loops in PDB to fit the structure

- Energy minimisation of the loop

23
Q

What type of loop is the best to predict?

A

Short loops (<6 residues), well predicted by all methods

24
Q

After you substitute the sequence from known structure with the unknown structure and fit loops in what is the next step of homology modelling?

A

Pack side chains - given the backbone predict psi, phi, omega, chi
Only allowed angles need to be sampled

25
Q

What are rotamer libraries?

A

Library of amino acid conformations - used for side chain packing in homology modelling

26
Q

What is fold recognition (threading)?

A

Sequencing searching using secondary structure if no MSA can be found

27
Q

What is a Hidden markov model

A

An algorithm that identifies distant homologues by matching secondary structure and sequence.

28
Q

Give an examples of a programme that use HMM for protein structure prediction.

A

HHPRED

29
Q

What is HHPRED?

A

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

30
Q

Briefly what does Phyre do?

A

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

31
Q

What does phyrealarm do?

A

Checks programs very week for new hits as the database is constantly added to

32
Q

What does Phyre investigator do?

A

Give information on which parts the prediction are reliable, what is functionally important and what residues are involved in protein interactions

33
Q

What does the accuracy of a good template rely on?

A

A good MSA

34
Q

When are ab initio methods required in protein structure prediction?

A

When no known templates are available

‘template free prediction’

35
Q

What is an immunoglobulin fold?

A

Pair of stacked beta sheets running antiparallel with disulphide bonds in between

36
Q

How many CDR classical structure (conical forms) are there?

A

2 - long and short

37
Q

What does HAMA stand for?

A

Human Anti Mouse Antibody response

38
Q

What is HAMA?

A

Mouse antibodies leading to an immune response in humans

39
Q

What is a chimeric antibody?

A

Human except for the V domains

40
Q

What is a full humanised antibody

A

Human except for the CDR domains

- steric clases exist between CDR and antibody so antibody has to be adapted an these changes are patented

41
Q

What is Rosetta antibody?

A

Program for building 3D model for antibody

42
Q

How does rosetta antibody work?

A

Take sequence of antibody
Homology model variable regions
Put together to create beta barrel
Graft on canoical loops

43
Q

What is an antibody fragment?

A

The variable regions of the antibody. these can be used in isolation and linked with an artificial disulphide bond

44
Q

Which CDR is hardest to model?

A

H3

Biotechnology (13 decks)

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