by Florencio Pazos, 1997
Structure prediction form sequence
"in
practice"
Interpretación de Resultados.
Formato de ficheros.
PHD_sec,_acc
............
.............
...............
* *
* Abbreviations: PHDsec *
* ~~~~~~~~~~~~~~~~~~~~~ *
* *
* sequence: *
* AA : amino acid sequence *
* secondary structure: *
* HEL: H=helix, E=extended (sheet), blank=other (loop) *
* PHD: Profile network prediction HeiDelberg *
* Rel: Reliability index of prediction (0-9) *
* detail: *
* prH: 'probability' for assigning helix *
* prE: 'probability' for assigning strand *
* prL: 'probability' for assigning loop *
* note: the 'probabilites' are scaled to the interval 0-9, e.g.,*
* prH=5 means, that the first output node is 0.5-0.6 *
* subset: *
* SUB: a subset of the prediction, for all residues with an expected *
* average accuracy > 82% (tables in header) *
* note: for this subset the following symbols are used: *
* L: is loop (for which above " " is used) *
* ".": means that no prediction is made for this residue, as the *
* reliability is: Rel < 5 *
* *
* Abbreviations: PHDacc *
* ~~~~~~~~~~~~~~~~~~~~~ *
* *
* SS : secondary structure *
* HEL: H=helix, E=extended (sheet), blank=other (loop) *
* solvent accessibility: *
* 3st: relative solvent accessibility (acc) in 3 states: *
* b = 0-9%, i = 9-36%, e = 36-100%. *
* PHD: Profile network prediction HeiDelberg *
* Rel: Reliability index of prediction (0-9) *
* O_3: observed relative acc. in 3 states: B, I, E *
* note: for convenience a blank is used intermediate (i). *
* P_3: predicted relative accessibility in 3 states *
* 10st:relative accessibility in 10 states: *
* = n corresponds to a relative acc. of n*n % *
* subset: *
* SUB: a subset of the prediction, for all residues with an expected *
* average correlation > 0.69 (tables in header) *
* note: for this subset the following symbols are used: *
* "I": is intermediate (for which above " " is used) *
* ".": means that no prediction is made for this residue, as the *
* reliability is: Rel < 4 *
* *
****************************************************************************
* *
* protein: 5p21 length 166 *
* *
....,....1....,....2....,....3....,....4....,....5....,....6 <- numeración
AA |MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG| <- secuencia
OBS sec | EEEEEEEE HHHHHHHHHH EEEEEEEEEE EEEEEEEEEE | Compromiso entre predecir muchos residuos y
PHD sec | EEEEEEE HHHHHEHHHH EEEEEEEEEEEEE EEEEEEE | <- quedarse con los de alta accuracy que logra un acierto global de 72%.
Rel sec |955999995478764157631124433554767425443347999817259999731677| <- Confianza.
detail:
prH sec |000000000001123467754345652101110000001100000000000000000111| <- Salida de la red para helice.
prE sec |027999996310000011134432112221011256665567999851479998854100| <- Salida de la red para beta.
prL sec |962000002688876421000111235666777642223321000148520000134788| <- Salida de la red para loop.
subset: SUB sec |LLEEEEEEE.LLLL..HHH........LL.LLL..E.....EEEEE.L.EEEEEE..LLL|
accessibility:
3st: O_3 acc |eeeb bbbbbbeeb b bb b eeee eeeee eeee eee ebee eb b b bbb |
P_3 acc |eeebebbbbbeeebbebbbbbebbeeebeeebebbbeeebeeebebeeeebebebbbbbb| <- Prediccón accesibilidad.
10st: OBS acc |866250000027804243003234786658998738667476647188560313030015| (b: buried; e: exposed)
PHD acc |977060000077700600000600777067706000667077606077760606000000|
Rel acc |454317787523323123745233444315401015104244152133524261730142| <- Confianza.
subset: SUB acc |eee..bbbbb........bbb...eee..ee....b..e.ee.b....e.b.b.b...b.|
....,....7....,....8....,.........
AA |QEEYSAMRDQYMRTGEGFLCVFAIN.........
.......................
..............
......
PHD_htm
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--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION: SYMBOLS
--- AA : amino acid in one-letter code
--- PHD htm : HTM's predicted by the PHD neural network
--- system (H=HTM, ' '=not HTM)
--- Rel htm : Reliability index of prediction (0-9, 0 is low)
--- detail : Neural network output in detail
--- prH htm : 'Probability' for assigning a helical trans-
--- membrane region (HTM)
--- prL htm : 'Probability' for assigning a non-HTM region
--- note: 'Probabilites' are scaled to the interval
--- 0-9, e.g., prH=5 means, that the first
--- output node is 0.5-0.6
--- subset : Subset of more reliable predictions
--- SUB htm : All residues for which the expected average
--- accuracy is > 82% (tables in header).
--- note: for this subset the following symbols are used:
--- L: is loop (for which above ' ' is used)
--- '.': means that no prediction is made for this,
--- residue as the reliability is: Rel < 5
--- other : predictions derived based on PHDhtm
--- PHDFhtm : filtered prediction, i.e., too long HTM's are
--- split, too short ones are deleted
--- PHDRhtm : refinement of neural network output
--- PHDThtm : topology prediction based on refined model
--- symbols used:
--- i: intra-cytoplasmic
--- T: transmembrane region
--- o: extra-cytoplasmic
---
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION
....,....1....,....2....,....3....,....4....,....5....,....6 <- Numeración.
AA |EPVSLTLALLLGGLTMGGIAAGIGTGTTALMATQQFQQLQAAVQDDLREVEKSISNLEKS| <- Secuencia.
PHD htm | | <- Compromiso entre predecir muchos residuos y
Rel htm |999999999998888877777678999999999999999999999999999999999999| <| accuracy tal que accuracy ~=95% (ver abajo)
detail: | | |- Confianza.
prH htm |000000000000000011111110000000000000000000000000000000000000| <- Salida de la red para hélice transmembrana
prL htm |999999999999999988888889999999999999999999999999999999999999| <- " " " " " NO hélice transmembrana
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....7....,....8....,....9....,....10...,....11...,....12
AA |LTSLSEVVLQNRRGLDLLFLKEGGLCAALKEECCFYADHTGLVRDSMAKLRERLNQRQKL|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....13...,....14...,....15...,....16...,....17...,....18
AA |FESTQGWFEGLFNRSPWFTTLISTIMGPLIVLLMILLFGPCILNRLVQFVKDRISVVQAL|
PHD htm | HHHHHHHHHHHHHHHHHHHHHHHHHHHHH | <- Helice transmembrana predicha.
Rel htm |999999999999998642046778888888888888888888765530135677889999|
detail: | |
prH htm |000000000000000123578889999999999999999999887764432111000000|
prL htm |999999999999999876421110000000000000000000112235567888999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLL....HHHHHHHHHHHHHHHHHHHHHHHHHH....LLLLLLLLLL|
other: | |
PHDFhtm | HHHHHHHHHHHHHHHHHHHHHHHHHHHHH |
PHDRhtm | HHHHHHHHHHHHHHHHHHHHH |
PHDThtm |ooooooooooooooooooooooTTTTTTTTTTTTTTTTTTTTTiiiiiiiiiiiiiiiii|
---
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END
---
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