Example for PHD output
Sequence: prio_human (Swissprot)
MAJOR PRION PROTEIN PRECURSOR (PRP)
OUTPUT
Publication to reference in reporting results:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rost, Burkhard; Sander, Chris: Prediction of protein structure
at better than 70% accuracy. J. Mol. Biol., 1993, 232, 584-599.
Rost, Burkhard; Sander, Chris: Combining evolutionary information
and neural networks to predict protein secondary structure.
Proteins, 1994, 19 (No. 1), 55-72.
Rost, Burkhard; Sander, Chris: Conservation and Prediction of
Solvent Accessibility in Protein Families. Proteins, 1994,
in press.
Some statistics:
~~~~~~~~~~~~~~~~
Percentage of amino acids:
+--------------+--------+--------+--------+--------+--------+
| AA: | G | P | S | Q | V |
| % of AA: | 17.8 | 6.7 | 5.9 | 5.9 | 5.5 |
+--------------+--------+--------+--------+--------+--------+
| AA: | Y | T | N | M | L |
| % of AA: | 5.1 | 5.1 | 4.7 | 4.7 | 4.7 |
+--------------+--------+--------+--------+--------+--------+
| AA: | R | K | H | A | W |
| % of AA: | 4.3 | 4.0 | 4.0 | 4.0 | 3.6 |
+--------------+--------+--------+--------+--------+--------+
| AA: | I | E | F | D | C |
| % of AA: | 3.6 | 3.6 | 2.8 | 2.4 | 1.6 |
+--------------+--------+--------+--------+--------+--------+
Percentage of secondary structure predicted:
+--------------+--------+--------+--------+
| SecStr: | H | E | L |
| % Predicted: | 10.7 | 18.2 | 71.1 |
+--------------+--------+--------+--------+
According to the following classes:
all-alpha: %H>45 and %E< 5; all-beta : %H<5 and %E>45
alpha-beta : %H>30 and %E>20; mixed: rest,
this means that the predicted class is: mixed class
PHD output for your protein:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fri Jun 10 15:18:27 1994
For secondary structure prediction:
Jury on: 10 different architectures (version 5.94 ).
For solvent accessibility prediction:
Jury on: 5 different architectures (version 5.94 ).
Note: differently trained architectures, i.e., different versions can
result in different predictions.
About the protein:
------------------
HEADER prio_human.gcg
COMPND
SOURCE
AUTHOR
SEQLENGTH 253
NCHAIN 1 chain(s) in prio_human data set
NALIGN 48
(=number of aligned sequences in HSSP file)
Abbreviations:
--------------
secondary structure : H=helix, E=extended (sheet), blank=rest (loop)
accessibility :
3st: relative solvent accessibility (acc) in 3 states:
b = 0-9%, i = 9-36%, e = 36-100%.
10st: relative solvent acc. in 10 states
= n corresponds to a relative acc. of n*n %
AA: amino acid sequence
OBS: values for experimentally observed 3D structures
OBS sec: DSSP classification of secondary structure
OBS acc: DSSP estimat of relative solvent accessibility area
O_3 acc: observed relative accessibility in 3 states: B, I, E
Note: a blank is used for intermediate (i)
PHD: Profile network prediction HeiDelberg
PHD sec: prediction of secondary structure in three states
PHD acc: prediction of solvent accessibility in 10 states
P_3 acc: predicted relative accessibility in 3 states
Rel: Reliability index of prediction (0-9)
Rel sec: reliability of secondary structure prediction
Rel sec: reliability of accessibility prediction
detail:
prH sec: 'probability' for assigning helix
prE sec: 'probability' for assigning strand
prL:sec: 'probability' for assigning loop
Note: the 'probabilites' are scaled to the interval 0-9,
i.e. prH=5 means, that the signal at the first
output node is 0.5-0.6.
subset:
SUB: a subset of the prediction, for all residues with
a reliablity > n, with the following choices:
SUB sec: for secondary structure prediction n >= 5, which
corresponds to an expected accuracy > 82% (see
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
SUB acc: for accessibility prediction n >= 4, which
corresponds to an expected correlation coefficient
> 0.69% (see 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: prio length 253
....,....1....,....2....,....3....,....4....,....5....,....6
AA |MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP|
PHD sec | EEEEEEEEEEE |
Rel sec |983211699899885157889998887788556886678877647677876567766654|
detail:
prH sec |001222000000000000000000111101222111111111221211111221111122
prE sec |002334788888886421000000000000000000000000000000000000000000
prL sec |985443100000012477888998888888767887778888767788877777777776
subset: SUB sec |LL....EEEEEEEEE.LLLLLLLLLLLLLLLLLLLLLLLLLLL.LLLLLLLLLLLLLLL.|
ACC:
3st: P_3 acc |eeebbbbbbbbbbbbbbeee eeeeeeeeb e bbe ebeb eebee eeeb b b b|
10st: PHD acc |967000000000000007665667666860565006556060566066558860505030
Rel acc |515413599998742104212224102410211002222021211021113311102200
subset: SUB acc |e.eb..bbbbbbbb...e.....e...e................................|
....,....7....,....8....,....9....,....10...,....11...,....1
AA |HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA|
PHD sec | |
Rel sec |556543545687444567754445787553244453568899998789887566545676|
detail:
prH sec |221233222111222221123222111223433323220000000110011211222111
prE sec |000000000000000000000000000000000000000000000000000010000000
prL sec |777666666787666677766666788765566666678899998888887777767787
subset: SUB sec |LLLL..L.LLLL...LLLLL...LLLLLL.....L.LLLLLLLLLLLLLLLLLLL.LLLL|
ACC:
3st: P_3 acc | b b b b b b b e bbb b e bb b bbbe eeeeeeeeeee eebbbbbbbbb|
10st: PHD acc |505050505050305630005036500530500065366668766676366000000000
Rel acc |221223201010001101012301110103101122021124411141022103331222
ACC:
2...,....13...,....14...,....15...,....16...,....17...,....1
AA |VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV|
PHD sec | EEEE EEEEEE|
Rel sec |567755311344445665677778778555587455899355432765678995554168|
detail:
prH sec |111122344322332111110011111111001210000000000112110000000000
prE sec |100000000010000012111000000122210122100367664101100002676578
prL sec |777766544566666776678878878766687666888522335776678997223421
subset: SUB sec |LLLLLL........LLLLLLLLLLLLLLLLLLL.LLLLL.EE...LLLLLLLLLEE..EE|
ACC:
3st: P_3 acc | bbb bb bbbeb beb bebb e eeebbeebb bbe bbb bbee eeeeebbbbbb|
10st: PHD acc |500050050006050605060057566600670055206500040066567666000000
Rel acc |113211521142021301020224222200241123321241130034233203342299
ACC:
8...,....19...,....20...,....21...,....22...,....23...,....2
AA |NITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPV|
PHD sec |EEEEEEEEEEE HHHHHHHHHHHHHHHHHHHHHHHHHHH EEEEE E|
Rel sec |999988588653788762115688999999998698996699986179974688829967|
detail:
prH sec |000000000000000000136788999999998788897799987410000000000000
prE sec |999988688773110123320000000000000000000000001100016788840018
prL sec |000011311225888875432200000000000100002200001489973110059971
subset: SUB sec |EEEEEEEEEEE.LLLLL...HHHHHHHHHHHHHHHHHHHHHHHHH.LLLL.EEEE.LLLE|
ACC:
3st: P_3 acc |bbbbee bbeeeeeeee eeebbebbe bbebbbbbbbeeeeeb eeeebbbbbebbbb|
10st: PHD acc |000066300666667675766006007500700000006766605577860000080000
Rel acc |375942003323347172543014675499729930014933505286621233540006
subset: SUB acc |.bbbe........ee.e.ee...ebbeibbe.bb....ee..e.i.eee.....be...b|
4...,....25...,....26...,....27...,....28...,....29...,....3
AA |ILLISFLIFLIVG|
PHD sec |EEEE EEEE |
Rel sec |8885111124529
detail:
prH sec |0012344432100
prE sec |8886212456650
prL sec |0001443100139
subset: SUB sec |EEEE......E.L|
ACC:
3st: P_3 acc |bbbbbbbbbbb e|
10st: PHD acc |0000000000059
Rel acc |9999699896229
subset: SUB acc |bbbbbbbbbb..e|