METHOD about: | ../../doc/explain_methods.html#PX_about_phd |
METHOD url: | PHD |
METHOD quote: | B Rost:: PHD: predicting one-dimensional protein structure by profile based neural networks. Methods in Enzymology, 266, 525-539, 1996. |
TYPE : | sec |
NPROT : | 373 |
NWEEKS : | 78 |
AVE_Q3 : | 71.5 |
AVE_SOV: | 67.7 |
NOTE 1 : | here ALL results obtained for phd are given, i.e. NOT those for a common subset! |
NOTE 2 : | all proteins evaluated had no SIGNIFICANT sequence identity to any protein of previously known structure! |
type | date | sots | id | Q3 | Q3H%o | Q3H%p | Q3E%o | Q3E%p | Q3L%o | Q3L%p | sov | sovH | sovE | sovL | BAD | info | infoO | infoP | corrH | corrE | corrL | class | contDH | contDE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
sec | 2004_04_28 | dssp | psum | 71.4 | 75 | 77 | 61 | 64 | 73 | 69 | 67.6 | 67.9 | 70.7 | 64.0 | 4.0 | 0.30 | 0.30 | 0.30 | 0.63 | 0.53 | 0.49 | 7962.4 | 8.9 | 7.6 |
sec | 2004_04_28 | dssp | sig | 12.4 | 36 | 36 | 37 | 39 | 17 | 15 | 17.2 | 31.3 | 28.4 | 18.0 | 7.1 | 0.16 | 0.17 | 0.16 | 0.28 | 0.31 | 0.19 | 7893.5 | 9.6 | 9.8 |
sec | 2004_04_28 | dssp | errsig | 0.64 | 1 | 1 | 1 | 2 | 0.89 | 0.79 | 0.89 | 1.6 | 1.4 | 0.93 | 0.37 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 408.7 | 0.49 | 0.50 |
Type | Method | Month | Nprot | Average Q3 for month | File with details for month |
---|---|---|---|---|---|
sec | phd | ALL | 373 | 71.5 | |
sec | phd | 2001_04 | 1 | 75.5 | old/2001_04_phd.html |
sec | phd | 2003_07 | 5 | 76.7 | old/2003_07_phd.html |
sec | phd | 2003_08 | 5 | 60.4 | old/2003_08_phd.html |
sec | phd | 2003_11 | 22 | 74.5 | old/2003_11_phd.html |
sec | phd | 2003_12 | 19 | 72.8 | old/2003_12_phd.html |
sec | phd | 2004_01 | 11 | 73.2 | old/2004_01_phd.html |
sec | phd | 2004_02 | 19 | 72.3 | old/2004_02_phd.html |
sec | phd | 2004_03 | 12 | 73.5 | old/2004_03_phd.html |
sec | phd | ALL | 373 | 71.5 |
psum | percentage over all proteins |
sig | standard deviation |
errsig | significant difference (to distinguish between two methods) |
type | prediction type |
date | date when added [yyyy_mm_dd] |
sots | standard of truth |
id | identifier of protein |
Q3 | three-state per-residue accuracy (percentage of correctly predicted residues) |
Q3H%o | correctly predicted helix residues (percentage of helix observed) |
Q3H%p | correctly predicted helix residues (percentage of helix predicted) |
Q3E%o | correctly predicted strand residues (percentage of helix observed) |
Q3E%p | correctly predicted strand residues (percentage of helix predicted) |
Q3L%o | correctly predicted loop residues (percentage of helix observed) |
Q3L%p | correctly predicted loop residues (percentage of helix predicted) |
sov | per segment accuracy (three states) |
sovH | per segment accuracy for helix residues |
sovE | per segment accuracy for strand residues |
sovL | per segment accuracy for non-regular residues |
BAD | percentage of confused HELIX/STRAND residues (helix predicted as strand, strand predicted as helix) |
infoO | information index accuracy (percentage of observed) |
infoP | information index accuracy (percentage of predicted) |
corrH | Matthews correlation index for helix |
corrE | Matthews correlation index for strand |
corrL | Matthews correlation index for loop |
var | variance over all proteins (1/N-1)*( score(i) - |
sig | sigma (standard deviation) over all proteins (sqrt[var]) |
errsig | significant differences ( standard dev / sqrt(Nprot) ) |