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|
********************************************************************************
* *
* 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, 55-72. *
* *
********************************************************************************
* *
* Some statistics: *
* ~~~~~~~~~~~~~~~~ *
* *
* Percentage of amino acids: *
* *
* +--------------+--------+--------+--------+--------+--------+
* | AA: | T | C | P | I | A |
* | % of AA: | 13.0 | 13.0 | 10.9 | 10.9 | 10.9 |
* +--------------+--------+--------+--------+--------+--------+
* | AA: | G | N | Y | V | S |
* | % of AA: | 8.7 | 6.5 | 4.3 | 4.3 | 4.3 |
* +--------------+--------+--------+--------+--------+--------+
* | AA: | R | L | F | E | D |
* | % of AA: | 4.3 | 2.2 | 2.2 | 2.2 | 2.2 |
* +--------------+--------+--------+--------+--------+--------+
* *
* Percentage of secondary structure predicted/observed: *
* *
* +--------------+--------+--------+--------+
* | SecStr: | H | E | L |
* | % Predicted: | 0.0 | 6.5 | 93.5 |
* +--------------+--------+--------+--------+
* | SecStr: | H | E | L |
* | % Observed: | 47.8 | 8.7 | 43.5 |
* +--------------+--------+--------+--------+
* *
* 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: *
* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ *
* *
* *
* Thu Mar 1 21:40:00 2001 *
* *
* Jury on: 1 different architectures (version 5.94_317 ). *
* Note: differently trained architectures, i.e., different versions can *
* result in different predictions. *
* *
* *
********************************************************************************
* *
* *
* *
* About the protein: *
* ------------------ *
* *
* *
* HEADER PLANT SEED PROTEIN *
* COMPND CRAMBIN *
* SOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED *
* AUTHOR W.A.HENDRICKSON,M.M.TEETER *
* SEQLENGTH 46 *
* NCHAIN 1 chain(s) in 1crn data set *
* NALIGN 11 *
* (=number of aligned sequences in HSSP file) *
* *
* *
********************************************************************************
* *
* *
* *
* Abbreviations: *
* -------------- *
* *
* secondary structure : H=helix, E=extended (sheet), blank=rest (loop) *
* *
* AA: amino acid sequence *
* 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, *
* 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 *
* 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 *
* *
* *
********************************************************************************
* *
* *
* protein: 1crn length 46 *
* *
....,....1....,....2....,....3....,....4....,....5....,....6
AA |TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN|
Obs | EE HHHHHHHHHHH HHHHHHHH EE GGG |
PHD | EEE |
Rel |9999999998433445789999962233599743337799999999
detail:
prH-|0000000001211121100000011101100000000100000000
prE-|0000000000122211000000013322100166630000000000
prL-|9999999998656657789999974565799823368899999999
subset: SUB |LLLLLLLLLL.....LLLLLLLLL....LLLL....LLLLLLLLLL|
* *
********************************************************************************
* *
* *
* *
* Performance accuracy of the prediction *
* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ *
* *
* *
+-----------------+------------------------------------------------+-------------------+
| 1crn : 46 | method:jury | segments |
+-----------------+------------------------------------------------+-------------------+
| number of residues with H,E,C | % of DSSP | % of Net | number |av length|
+--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+
| |net H |net E |net C |sum DS| H | E | C | H | E | C |DSSP| Net|DSSP| Net|
+--------+------+------+------+------+-----+-----+-----+---+---+---+----+----+----+----+
| DSSP H | 0| 0| 22| 22| 0.0| 0.0|100.0| 0| 0| 51| 2| 0| 9.5| 0.0|
| DSSP E | 0| 2| 2| 4| 0.0| 50.0| 50.0| 0| 66| 4| 2| 1| 2.0| 3.0|
| DSSP C | 0| 1| 19| 20| 0.0| 5.0| 95.0| 0| 33| 44| 7| 2| 1.6|21.5|
+--------+------+------+------+------+-----+-----+-----+---+-+-+---+----+----+----+----+
| sum Net| 0| 3| 43| 46|corH |corE |corC | Q3 | SQ | 11| 3| 3.1|15.3|
| |0.00 |0.54 |0.05 | 45.7| 48.3| |
+---------+--------------------------+++---+-----+-----++****+*****+-------------------+
| segments| % of observed || % of predicted | information |
+---------+------+------+------+------++------+------+------+------+---------+---------+
| measure | % H | % E | % L | sum || % H | % E | % L | sum | I %obs | I %pred |
+---------+------+------+------+------++------+------+------+------+---------+---------+
| SOV | 0.0 | 50.0 | 37.4 | 20.6 || 0.0 |100.0 | 28.1 | 32.8 |0.05 7%|0.22 35%|
+---------+------+------+------+------++------+------+------+------+---------+---------+
* *
* *
* *
* *
********************************************************************************
* *
* *
END
|
