DJ: references and formulas

Question 1

First generation secondary structure prediction methods

Answer 1

Chou and Fasman, 1974

Question 2

PSIPRED

Answer 2

Jones, 1999

Question 3

PHD

Answer 3

Rost and Sander, 1993

Question 4

DSSP

Answer 4

Define Secondary Structure of Proteins (Kabsch and Sander, 1983)

Question 5

GOR method

Answer 5

Garnier et al., 1978

Question 6

Backpropagation

Answer 6

Rumelhart et al., 1986

Question 7

Degree of solvent accessibility of an amino acid residue can be predicted accurately from an MSA

Answer 7

Benner and Gerloff, 1990

Question 8

Threading itself

Answer 8

Jones et al., 1992

Question 9

genTHREADER

Answer 9

Jones, 1999

Question 10

Normalisation of PSSM values

Answer 10

1/(1+e**-x)

Question 11

Matthew’s Correlation Coefficient (1975)

Answer 11

E.G. for a helix state:

p: patterns correctly assigned to helix
n: patterns correctly assigned to not helix
o: patterns incorrectly assigned to helix
u: patterns incorrectly assigned to not helix

Question 12

First NN to predict secondary structure

Answer 12

Qian and Sejnowski, 1988

Question 13

Searching for the optimum mapping of sequence to structure while optimizing the sum of pair interactions is NP-complete

Answer 13

Lathrop, 1994