Task 3 (MSUD)

Secondary structure

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Result

The results for ReProf and PsiPred predictions and the DSSP assignments are in the following folders:

/mnt/home/student/schillerl/MasterPractical/task3/reprof/

/mnt/home/student/schillerl/MasterPractical/task3/psipred/

/mnt/home/student/schillerl/MasterPractical/task3/dssp/

For P10775, ReProf was run with the protein sequence fasta file and position specific scoring matrices (PSSM) derived from big_80 and SwissProt (see /mnt/home/student/schillerl/MasterPractical/task3/pssm/) as input. The following tables show the comparison of the prediction results to the secondary structure assignment of DSSP. The f-measure is the harmonic mean of recall and precision, it gives a good indication for the quality of a classificator.

Comparison of ReProf prediction (fasta input) to DSSP assignment

secondary structure element	recall	precision	f-measure
H	0.719	0.585	0.645
E	0.211	0.500	0.296
L	0.616	0.654	0.635

Comparison of ReProf prediction (big_80 PSSM input) to DSSP assignment

secondary structure element	recall	precision	f-measure
H	0.944	0.889	0.916
E	0.649	0.685	0.667
L	0.826	0.866	0.846

Comparison of ReProf prediction (SwissProt PSSM input) to DSSP assignment

secondary structure element	recall	precision	f-measure
H	0.923	0.914	0.919
E	0.807	0.523	0.634
L	0.719	0.859	0.782

Predictions using a PSSM instead of a simple sequence have a considerably better quality. All methods predict helices better than loops and these better than beta sheets. The results of the run with the big_80 PSMM are better for E and L and only slightly worse than those using the SwissProt PSMM.

The percentages of correctly identified secondary structure (H, E or L) for the three methods are 61 %, 86 % and 82 %. So for the remaining sequences, the method with the best performance (usage of PSSM derived from big_80 as input for ReProf) is used.

Disordered protein

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Transmembrane helices

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Signal peptides

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GO terms

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