Hemochromatosis

Secondary Structure

In this task, secondary structure of proteins is predicted using the programs reProf and PsiPred. The results are then compared to the DSSP secondary structure assignments from corresponding crystal structures in the PDB. Thus, the following crystal structures were selected for comparison. The first priority for selection was to get the protein in its native state and not bound to another molecule. The other criteria were the quality of the structure and the alignment to the protein sequence(having one continous segment).

Uniprot			PDB
UID	Name	Length	ID	Resolution	Chain	Length
Q30201	Hereditary hemochromatosis protein	348	A16Z	2.60	A	275
P10775	Ribonuclease inhibitor	456	2BNH	2.30	A	457
Q9X0E6	Divalent-cation tolerance protein CutA	101	1VHF	1.54	A	113
Q08209	CAM-PRP catalytic subunit	521	1M63	2.80	A	372

In the next step, the output of the prediction programs and the DSSP assignments have to be made comparable. DSSP assigns 8 different classes of secondary structure, whereas reProf and PsiPred only predict helix(H), sheet(E) and loop(L or C). Therefore, H and G are mapped to H, E to E and all other DSSP classes to C.

DSSP: http://swift.cmbi.ru.nl/gv/dssp/ SOV:http://www.bio.ifi.lmu.de/files/Lehre/PRK_GoBi/material/home/Literatur/ZemlaVFR99.pdf
<math> Q_3 = \frac{correct predictions}{all predictions} = \frac{TP+FP}{TP + TN + FP + FN} </math>

Prediction methods
	Reprof + Sequence			Reprof + Big80			Reprof + SwissProt			Reprof + PDB			Psipred
Q3	0.76			0.81			0.86			0.84			0.84
SOV3	0.66			0.75			0.84			0.84			0.73
	Acc	Cov	F1	Acc	Cov	F1	Acc	Cov	F1	Acc	Cov	F1	Acc	Cov	F1
H	0.63	0.33	0.44	0.74	0.48	0.59	0.84	0.65	0.74	0.85	0.52	0.64	0.98	0.77	0.86
C	0.57	0.69	0.86	0.63	0.75	0.68	0.68	0.81	0.74	0.64	0.83	0.72	0.61	0.95	0.74
E	0.79	0.63	0.70	0.81	0.84	0.83	0.89	0.86	0.87	0.88	0.85	0.86	0.94	0.55	0.69

Protein	Method	Q3	SOV3
Q08209	ReProf	0.83	0.78
	Psipred	0.87	0.79
Q30201	ReProf	0.86	0.84
	Psipred	0.84	0.73
P10775	ReProf	0.91	0.93
	Psipred	0.93	0.94
Q9X0E6	ReProf	0.75	0.65
	Psipred	0.89	0.86

Hemochromatosis SS Alignments