Example for PHD output
Structure: 1hhp (PDB)
HIV-1 PROTEASE (BRU ISOLATE)
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), in press.
Some statistics:
~~~~~~~~~~~~~~~~
Percentage of amino acids:
+--------------+--------+--------+--------+--------+--------+
| AA: | I | G | L | T | V |
| % of AA: | 13.1 | 13.1 | 12.1 | 8.1 | 6.1 |
+--------------+--------+--------+--------+--------+--------+
| AA: | Q | P | K | R | E |
| % of AA: | 6.1 | 6.1 | 6.1 | 4.0 | 4.0 |
+--------------+--------+--------+--------+--------+--------+
| AA: | D | N | A | W | M |
| % of AA: | 4.0 | 3.0 | 3.0 | 2.0 | 2.0 |
+--------------+--------+--------+--------+--------+--------+
| AA: | F | C | Y | S | H |
| % of AA: | 2.0 | 2.0 | 1.0 | 1.0 | 1.0 |
+--------------+--------+--------+--------+--------+--------+
Percentage of secondary structure predicted/observed:
+--------------+--------+--------+--------+
| SecStr: | H | E | L |
| % Predicted: | 6.1 | 53.5 | 40.4 |
+--------------+--------+--------+--------+
| SecStr: | H | E | L |
| % Observed: | 7.1 | 48.5 | 44.4 |
+--------------+--------+--------+--------+
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
The class of the observed structure is: mixed class
PHD output for your protein:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fri Jun 10 15:30:51 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 HYDROLASE(ACID PROTEINASE)
COMPND HIV-1 PROTEASE (BRU ISOLATE)
SOURCE GENE OF THE HUMAN IMMUNODEFICIENCY VIRUS /HIV-1$
AUTHOR S.SPINELLI,P.M.ALZARI
SEQLENGTH 99
NCHAIN 1 chain(s) in 1hhp data set
NALIGN 58
(=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: 1hhp length 99
....,....1....,....2....,....3....,....4....,....5....,....6
AA |PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD|
OBS sec | EEEEE EEEEEE EEE EEEEEEE EEEEEEEEE|
PHD sec | EEEE EEEEEE EEEEEEE EEEEEE EEEEE EEEEEE |
Rel sec |945644266799995261277564258753113431168997643688736515566412|
detail:
prH sec |000000000000000000000000000112332110000000000000000000000000
prE sec |037766422899997424587676521012345654421001236788831246677644
prL sec |962233577100002575411212378865322234578898763211157742222355
subset: SUB sec |L.EE...LLEEEEEE.L..EEEE..LLLL........LLLLLL..EEEE.LL.EEEE...|
ACC:
3st: O_3 acc |eeeeeeee e ebebee e eb ee eeb beebe eeee e e eeee e eb b |
P_3 acc |ee e ee ebebebeeeeeebbbeebbeeebbee e eeeeeeebbbbbbbbbe ee e|
10st: OBS acc |996789984637061785837043578476030672839887585647799585824415
PHD acc |985736755606060686667000760076600765737976686000000000656757
Rel acc |963702641314342164236264420143342621707671443251451210524626
subset: SUB acc |ee.e..ei...e.e..ee..e.bbe...e..b.e..e.eee.ee..b.bb....e.ee.e|
....,....7....,....8....,....9....,....10...,....11...,....1
AA |QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF|
OBS sec |EEEEEE EEEEEEEEEE EE HHHHHHH |
PHD sec |EEEEEEE EEEEEEEE EEE HHHHHH E |
Rel sec |599998284379999983998112251789961253009
detail:
prH sec |000000000000000000000000114888974322100
prE sec |799998512688999983000445520000000011440
prL sec |200001486310000016998444364110024565449
subset: SUB sec |EEEEEE.L..EEEEEEE.LLL....L.HHHHH..L...L|
ACC:
3st: O_3 acc |e eb beeeebe bbbbe eeb bbe bbee eeeeee|
P_3 acc |ebebe eeee ebbbbbbe bbebbb ebbeeb ee ee|
10st: OBS acc |836051686817350101849623006502774768899
PHD acc |706065677756000000750060005600670567569
Rel acc |714352357713224210521235373315462126236
subset: SUB acc |e.e.e..eee....b...e....b.b...bee...e..e|