From phd@EMBL-Heidelberg.de Fri May 8 10:21:47 1998 Return-Path: phd@EMBL-Heidelberg.de From: phd@EMBL-Heidelberg.de Date: Fri, 8 May 1998 17:21:25 GMT To: karplus@cse.ucsc.edu Subject: Predict-Protein The following information has been received by the server: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ reference predict_h1529 (Fri May 8 19:19:47 MDT 1998) from karplus@cse.ucsc.edu password(###) resp HTML orig HTML prediction of: -secondary structure (PHDsec)- return msf format # fasta list >T0044 RNA-3'terminal phosphate cyclase MVKRMIALDG AQGEGGGQIL RSALSLSMIT GQPFTITSIR AGRAKPGLLR QHLTAVKAAT EICGATVEGA ELGSQRLLFR PGTVRGGDYR FAIGSAGSCT LVLQTVLPAL WFADGPSRVE VSGGTDNPSA PPADFIRRVL EPLLAKIGIH QQTTLLRHGF YPAGGGVVAT EVSPVASFNT LQLGERGNIV QMRGEVLLAG VPRHVAEREI ATLAGSFSLH EQNIHNLPRD QGPGNTVSLE VESENITERF FVVGEKRVSA EVVAAQLVKE VKRYLASTAA VGEYLADQLV LPMALAGAGE FTVAHPSCHL LTNIAVVERF LPVRFSLIET DGVTRVSIEG SHHHHHH ________________________________________________________________________________ The sequence was interpreted to be: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ MSF of: /home/phd/server/work/predict_h1529-29955.hssp from: 1 to: 347 /home/phd/server/work/predict_h1529-29955.aliRet MSF: 347 Type: P 8-May-98 19:19:5 Check: 3588 .. Name: predict_h152 Len: 347 Check: 6794 Weight: 1.00 Name: predict_h152 Len: 347 Check: 6794 Weight: 1.00 // 1 50 predict_h152 MVKRMIALDG AQGEGGGQIL RSALSLSMIT GQPFTITSIR AGRAKPGLLR predict_h152 MVKRMIALDG AQGEGGGQIL RSALSLSMIT GQPFTITSIR AGRAKPGLLR 51 100 predict_h152 QHLTAVKAAT EICGATVEGA ELGSQRLLFR PGTVRGGDYR FAIGSAGSCT predict_h152 QHLTAVKAAT EICGATVEGA ELGSQRLLFR PGTVRGGDYR FAIGSAGSCT 101 150 predict_h152 LVLQTVLPAL WFADGPSRVE VSGGTDNPSA PPADFIRRVL EPLLAKIGIH predict_h152 LVLQTVLPAL WFADGPSRVE VSGGTDNPSA PPADFIRRVL EPLLAKIGIH 151 200 predict_h152 QQTTLLRHGF YPAGGGVVAT EVSPVASFNT LQLGERGNIV QMRGEVLLAG predict_h152 QQTTLLRHGF YPAGGGVVAT EVSPVASFNT LQLGERGNIV QMRGEVLLAG 201 250 predict_h152 VPRHVAEREI ATLAGSFSLH EQNIHNLPRD QGPGNTVSLE VESENITERF predict_h152 VPRHVAEREI ATLAGSFSLH EQNIHNLPRD QGPGNTVSLE VESENITERF 251 300 predict_h152 FVVGEKRVSA EVVAAQLVKE VKRYLASTAA VGEYLADQLV LPMALAGAGE predict_h152 FVVGEKRVSA EVVAAQLVKE VKRYLASTAA VGEYLADQLV LPMALAGAGE 301 347 predict_h152 FTVAHPSCHL LTNIAVVERF LPVRFSLIET DGVTRVSIEG SHHHHHH predict_h152 FTVAHPSCHL LTNIAVVERF LPVRFSLIET DGVTRVSIEG SHHHHHH ________________________________________________________________________________ Result of COILS prediction (Andrei Lupas): ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ no coiled-coil above 0.5 ________________________________________________________________________________ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Secondary structure prediction by PHDsec: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Author: Burkhard Rost EMBL, Heidelberg, FRG Meyerhofstrasse 1, 69 117 Heidelberg Internet: Rost@EMBL-Heidelberg.DE All rights reserved. About the network method ~~~~~~~~~~~~~~~~~~~~~~~ The network procedure is described in detail in: 1) Rost, Burkhard; Sander, Chris: Prediction of protein structure at better than 70% accuracy. J. Mol. Biol., 1993, 232, 584-599. A brief description is given in: Rost, Burkhard; Sander, Chris: Improved prediction of protein secondary structure by use of se- quence profiles and neural networks. Proc. Natl. Acad. Sci. U.S.A., 1993, 90, 7558-7562. The PHD mail server is described in: 2) Rost, Burkhard; Sander, Chris; Schneider, Reinhard: PHD - an automatic mail server for protein secondary structure prediction. CABIOS, 1994, 10, 53-60. The latest improvement steps (up to 72%) are explained in: 3) Rost, Burkhard; Sander, Chris: Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 1994, 19, 55-72. To be quoted for publications of PHD output: Papers 1-3 for the prediction of secondary structure and the pre- diction server. About the input to the network ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The prediction is performed by a system of neural networks. The input is a multiple sequence alignment. It is taken from an HSSP file (produced by the program MaxHom: Sander, Chris & Schneider, Reinhard: Database of Homology-Derived Structures and the Structural Meaning of Sequence Alignment. Proteins, 1991, 9, 56-68. For optimal results the alignment should contain sequences with varying degrees of sequence similarity relative to the input protein. The following is an ideal situation: +-----------------+----------------------+ | sequence: | sequence identity | +-----------------+----------------------+ | target sequence | 100 % | | aligned seq. 1 | 90 % | | aligned seq. 2 | 80 % | | ... | ... | | aligned seq. 7 | 30 % | +-----------------+----------------------+ Estimated Accuracy of Prediction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A careful cross validation test on some 250 protein chains (in total about 55,000 residues) with less than 25% pairwise sequence identity gave the following results: ++================++-----------------------------------------+ || Qtotal = 72.1% || ("overall three state accuracy") | ++================++-----------------------------------------+ +----------------------------+-----------------------------+ | Qhelix (% of observed)=70% | Qhelix (% of predicted)=77% | | Qstrand(% of observed)=62% | Qstrand(% of predicted)=64% | | Qloop (% of observed)=79% | Qloop (% of predicted)=72% | +----------------------------+-----------------------------+ .......................................................................... These percentages are defined by: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | number of correctly predicted residues |Qtotal = --------------------------------------- (*100) | number of all residues | | no of res correctly predicted to be in helix |Qhelix (% of obs) = -------------------------------------------- (*100) | no of all res observed to be in helix | | | no of res correctly predicted to be in helix |Qhelix (% of pred)= -------------------------------------------- (*100) | no of all residues predicted to be in helix .......................................................................... Averaging over single chains ~~~~~~~~~~~~~~~~~~~~~~~~~~~ The most reasonable way to compute the overall accuracies is the above quoted percentage of correctly predicted residues. However, since the user is mainly interested in the expected performance of the prediction for a particular protein, the mean value when averaging over protein chains might be of help as well. Computing first the three state accuracy for each protein chain, and then averaging over 250 chains yields the following average: +-------------------------------====--+ | Qtotal/averaged over chains = 72.2% | +-------------------------------====--+ | standard deviation = 9.3% | +-------------------------------------+ .......................................................................... Further measures of performance ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matthews correlation coefficient: +---------------------------------------------+ | Chelix = 0.63, Cstrand = 0.53, Cloop = 0.52 | +---------------------------------------------+ .......................................................................... Average length of predicted secondary structure segments: . +------------+----------+ . | predicted | observed | +-----------+------------+----------+ | Lhelix = | 10.3 | 9.3 | | Lstrand = | 5.0 | 5.3 | | Lloop = | 7.2 | 5.9 | +-----------+------------+----------+ .......................................................................... The accuracy matrix in detail: +---------------------------------------+ | number of residues with H, E, L | +---------+------+------+------+--------+ | |net H |net E |net L |sum obs | +---------+------+------+------+--------+ | obs H |12447 | 1255 | 3990 | 17692 | | obs E | 949 | 7493 | 3750 | 12192 | | obs L | 2604 | 2875 |19962 | 25441 | +---------+------+------+------+--------+ | sum Net |16000 |11623 |27702 | 55325 | +---------+------+------+------+--------+ Note: This table is to be read in the following manner: 12447 of all residues predicted to be in helix, were observed to be in helix, 949 however belong to observed strands, 2604 to observed loop regions. The term "observed" refers to the DSSP assignment of secondary structure calculated from 3D coordinates of experimentally determined structures (Dictionary of Secondary Structure of Proteins: Kabsch & Sander (1983) Biopolymers, 22, 2577-2637). Position-specific reliability index ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The network predicts the three secondary structure types using real numbers from the output units. The prediction is assigned by choosing the maximal unit ("winner takes all"). However, the real numbers contain additional information. E.g. the difference between the maximal and the second largest output unit can be used to derive a "reliability index". This index is given for each residue along with the prediction. The index is scaled to have values between 0 (lowest reliability), and 9 (highest). The accuracies (Qtot) to be expected for residues with values above a particular value of the index are given below as well as the fraction of such residues (%res).: +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | index| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | | %res |100.0| 99.2| 90.4| 80.9| 71.6| 62.5| 52.8| 42.3| 29.8| 14.1| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | | | | | | | | | | | | | Qtot | 72.1| 72.3| 74.8| 77.7| 80.3| 82.9| 85.7| 88.5| 91.1| 94.2| | | | | | | | | | | | | +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | H%obs| 70.4| 70.6| 73.7| 77.1| 80.1| 83.1| 86.0| 89.3| 92.5| 96.4| | E%obs| 61.5| 61.7| 63.7| 66.6| 69.1| 71.7| 74.6| 77.0| 77.8| 68.1| | | | | | | | | | | | | | H%prd| 77.8| 78.0| 80.0| 82.6| 84.7| 86.9| 89.2| 91.3| 93.1| 95.4| | E%prd| 64.5| 64.7| 67.8| 71.0| 74.2| 77.6| 81.4| 85.1| 89.8| 93.5| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ The above table gives the cumulative results, e.g. 62.5% of all residues have a reliability of at least 5. The overall three-state accuracy for this subset of almost two thirds of all residues is 82.9%. For this subset, e.g., 83.1% of the observed helices are correctly predicted, and 86.9% of all residues predicted to be in helix are correct. .......................................................................... The following table gives the non-cumulative quantities, i.e. the values per reliability index range. These numbers answer the question: how reliable is the prediction for all residues labeled with the particular index i. +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | index| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | | %res | 8.8| 9.5| 9.3| 9.1| 9.7| 10.5| 12.5| 15.7| 14.1| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | | | | | | | | | | | | Qtot | 46.6| 50.6| 57.7| 62.6| 67.9| 74.2| 82.2| 88.3| 94.2| | | | | | | | | | | | +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ | H%obs| 36.8| 42.3| 49.5| 55.2| 61.7| 69.9| 78.8| 87.4| 96.4| | E%obs| 44.7| 44.5| 52.1| 55.4| 60.9| 68.0| 75.9| 81.0| 68.1| | | | | | | | | | | | | H%prd| 49.9| 52.5| 60.3| 64.2| 69.2| 77.5| 85.4| 89.9| 95.4| | E%prd| 41.7| 47.1| 53.6| 57.0| 64.0| 71.6| 78.8| 88.8| 93.5| +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ For example, for residues with Relindex = 5 64% of all predicted betha- strand residues are correctly identified. The resulting network (PHD) prediction is: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ PHD: Profile fed neural network systems from HeiDelberg ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prediction of: secondary structure, by PHDsec solvent accessibility, by PHDacc and helical transmembrane regions, by PHDhtm Author: Burkhard Rost EMBL, 69012 Heidelberg, Germany Internet: Rost@EMBL-Heidelberg.DE All rights reserved. The network systems are described in: PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599. B Rost & C Sander: Proteins, 1994, 19, 55-72. PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226. PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533. Some statistics ~~~~~~~~~~~~~~~ Percentage of amino acids: +--------------+--------+--------+--------+--------+--------+ | AA: | L | G | A | V | R | | % of AA: | 10.7 | 10.7 | 10.4 | 9.8 | 6.9 | +--------------+--------+--------+--------+--------+--------+ | AA: | E | T | S | P | I | | % of AA: | 6.9 | 6.3 | 6.3 | 4.9 | 4.9 | +--------------+--------+--------+--------+--------+--------+ | AA: | Q | H | F | N | D | | % of AA: | 4.0 | 4.0 | 3.7 | 2.3 | 2.3 | +--------------+--------+--------+--------+--------+--------+ | AA: | K | M | Y | C | W | | % of AA: | 2.0 | 1.4 | 1.2 | 0.9 | 0.3 | +--------------+--------+--------+--------+--------+--------+ Percentage of secondary structure predicted: +--------------+--------+--------+--------+ | SecStr: | H | E | L | | % Predicted: | 30.8 | 30.3 | 38.9 | +--------------+--------+--------+--------+ 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: alpha-beta PHD output for your protein ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fri May 8 19:19:56 1998 Jury on: 10 different architectures (version 5.94_317 ). Note: differently trained architectures, i.e., different versions can result in different predictions. About the protein ~~~~~~~~~~~~~~~~~ HEADER /home/phd/server/work/predict_h1529-2995 COMPND SOURCE AUTHOR SEQLENGTH 347 NCHAIN 1 chain(s) in predict_h1529-29955 data set NALIGN 1 (=number of aligned sequences in HSSP file) WARNING ~~~~~~~ Expected accuracy is about 72% if, and only if, the alignment contain sufficient information. For your sequence there was no homologue in the current version of Swissprot detected. This implies that the expected accuracy is about 6-10 percentage points lower ! 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 protein: predict length 347 ....,....1....,....2....,....3....,....4....,....5....,....6 AA |MVKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAAT| PHD sec | EEEEEEE HHHHHHHHHHHE E EEEEEE HHHHHHHHHHHHHH| Rel sec |932346672634458116446983443212572258861356788169999999999999| detail: prH sec |033221101122221457667886565342000000011221101479999999999999| prE sec |014567775111000000222000123444214568874211100000000000000000| prL sec |952110113656678442010003211112675320114567788520000000000000| subset: SUB sec |L....EEE.L...LL..H..HHH.......LL..EEEE..LLLLL.HHHHHHHHHHHHHH| ....,....7....,....8....,....9....,....10...,....11...,....12 AA |EICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVE| PHD sec |HHH EEEE EEEEE EE EEEEEEE E EHHHHHHHHH EEE| Rel sec |862553431245615577518866587414897417761121233222433338994699| detail: prH sec |875211111111010000000000000000000001122344355555654520000000| prE sec |000015654322246777641177211356888651003434521101112210002798| prL sec |023663234456742211258822688642001347774110012333232258996200| subset: SUB sec |HH.LL......LL.EEEEE.LLEELLL...EEE..LLL...............LLL.EEE| ....,....13...,....14...,....15...,....16...,....17...,....18 AA |VSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNT| PHD sec |EE HHHHHHHHHHHHHHH EEEEEE EEEEEE E | Rel sec |835899989991468999999998663541122442121125899769999734441323| detail: prH sec |000000000004678999999998775111111112210000000000000000011112| prE sec |862000000000000000000000001123455554334432000179998732223532| prL sec |037888888995321000000000122664333223444456899820000166664355| subset: SUB sec |E.LLLLLLLLL..HHHHHHHHHHHHH.L.............LLLLLEEEEEE........| ....,....19...,....20...,....21...,....22...,....23...,....24 AA |LQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLE| PHD sec | EEEEEEEEEEE HHHHHHHHHHHH E EEEEE| Rel sec |103566816543345764157147899999986177121113513389989999837899| detail: prH sec |232111011111111112101468899999987400113342243310010000000000| prE sec |332111146655556776320000000000000001342211000000000000168889| prL sec |335677831222221111467531100000012488433445655688989999831000| subset: SUB sec |...LLLL.EE....EEE..LL..HHHHHHHHHH.LL......L...LLLLLLLLL.EEEE| ....,....25...,....26...,....27...,....28...,....29...,....30 AA |VESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGE| PHD sec |EE EEEEEEEEEEE HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH E| Rel sec |726665379999975520089999999999999998679999999966444677721892| detail: prH sec |000111000000000001389999999999999998779999999877555787754100| prE sec |851102578889887654200000000000000000000000000000122111000005| prL sec |137776310000012234300000000000000001110000000021222101135883| subset: SUB sec |E.LLLL.EEEEEEEEE...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHH..LL.| ....,....31...,....32...,....33...,....34...,....35...,....36 AA |FTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIEGSHHHHHH| PHD sec |EEEE EEEEHHHHHE EEEEEE EEEEEE | Rel sec |67725762220122245521121499985489659999614454589| detail: prH sec |10000112222222466642111000000000000000001223210| prE sec |77852102323344321224434688886310268998742100000| prL sec |11137774443322211123454200012689720000245666689| subset: SUB sec |EEE.LLL.........HH......EEEEE.LLLEEEEEE...L.LLL| ________________________________________________________________________________ ________________________________________________________________________________ ----------------------------------------------------------------------------- --- PredictProtein: NEWS from January, 1997 --- --- --- --- Dear user, --- --- --- --- as of January 1, 1997, EMBL has effectively decided to not --- --- support the PredictProtein service by personal resources. I do --- --- maintain the program, so to speak, in my private time. However, --- --- my contract obliges me to do science, instead. Unfortunately, --- --- the computer environment at EMBL is at the same time starting --- --- to become increasingly unstable. Consequence of these two re- --- --- cent developments is that the PredictProtein service is not as --- --- stable as it was. --- --- --- --- I apologise for the problems this may cause. In particular, --- --- I apologise for my inability to reply to the 20-30 daily, per- --- --- sonal mails, and suggest to re-submit requests after 24 hours! --- --- --- --- Hoping that I shall find a more convenient solution for the --- --- future of the PredictProtein I remain with my best regards, --- --- --- --- Burkhard Rost --- ----------------------------------------------------------------------------- --- PredictProtein: NEWS from April, 1998 --- --- --- -------------------------------- --- --- MOVING PredictProtein --- --- There appears to be light on the horizon! PP will may be having --- --- many hickups over the next months (as I shall leave EMBL). How- --- --- ever, the server seems to have a fair chance of survival thanks --- --- to a major support that is being raised by Columbia University, --- --- New York, U.S.A.). I hope that this will settle the issue for --- --- the years to come ... --- -------------------------------- --- --- WARNING --- --- After a major rewriting of most of the PP code over the last, --- --- I am afraid that not all errors have been traced by me, yet. --- --- Thus, please have mercy and report any bug you'll encounter! --- --- THANKS, Burkhard Rost --- -------------------------------- --- --- NEW PREDICTION DEFAULTS --- --- * Coiled-coil regions: now by default the program COILS written by --- --- Andrei Lupas is run on your sequence. An output is returned if a --- --- coiled-coil region has been detected. --- --- * Functional sequence motifs: now by default the PROSITE database --- --- written by Amos Bairoch, Philip Bucher and Kay Hofmann is scanned --- --- for sequence motifs. An output is returned if any motif has been --- --- detected. --- -------------------------------- --- --- see http://www.embl-heidelberg.de/predictprotein/ppNews.html --- --- for a description of the following new options. --- --- NEW INPUT OPTION --- --- * Your input sequence(s) in FASTA-list format ("# FASTA list ") --- --- NEW OUTPUT OPTIONS --- --- * Return also BLASTP output ("return blast") --- --- * Return prediction additionally in RDB format ("return phd rdb") --- --- * Return topits hssp ("return topits hssp") --- --- * Return topits strip ("return topits strip") --- --- * Return topits own ("return topits own") --- --- * Return no coils ("return no coils") --- --- * Return no prosite ("return no prosite") --- -----------------------------------------------------------------------------