User:ChristopherW

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Revision as of 15:17, 4 September 2013

• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • * * * PHD: Profile fed neural network systems from HeiDelberg * * 10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT) * * * * 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 * * 10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT) * * * * Percentage of amino acids: * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | G | L | S | P | A | * * | % of AA: | 11.5 | 10.6 | 7.7 | 7.7 | 7.3 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | R | E | V | K | C | * * | % of AA: | 7.0 | 5.6 | 5.2 | 4.7 | 4.5 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | D | Q | T | F | Y | * * | % of AA: | 4.2 | 4.0 | 3.5 | 3.3 | 3.1 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | H | N | I | W | M | * * | % of AA: | 2.8 | 2.3 | 2.3 | 1.9 | 0.7 | * * +--------------+--------+--------+--------+--------+--------+ * * * * Percentage of helical trans-membrane predicted: * * +--------------+--------+--------+ * * | SecStr: | H | L | * * | % Predicted: | 0.0 | 100.0 | * * +--------------+--------+--------+ * * * **************************************************************************** * * * PHD output for your protein * * 10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)~~ * * * * Jury on: 4 different architectures (version 8.94_69 ). * * Note: differently trained architectures, i.e., different versions can * * result in different predictions. * * * **************************************************************************** * * * About the protein * * 10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)~~ * * * * HEADER * * COMPND * * SOURCE * * AUTHOR * * SEQLENGTH 426 * * NCHAIN 1 chain(s) in query data set * * NALIGN 55 * * (=number of aligned sequences in HSSP file) * * * * * * protein: query length 426 * * * --- --- 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 AA |MFRTKRSALVRRLWRSRAPGGEDEEEGAGGGGGGGELRGEGATDSRAHGAGGGGPGRAGC| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....7....,....8....,....9....,....10...,....11...,....12 AA |CLGKAVRGAKGHHHPHPPAAGAGAAGGAEADLKALTHSVLKKLKERQLELLLQAVESRGG| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....13...,....14...,....15...,....16...,....17...,....18 AA |TRTACLLLPGRLDCRLGPGAPAGAQPAQPPSSYSLPLLLCKVFRWPDLRHSSEVKRLCCC| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....19...,....20...,....21...,....22...,....23...,....24 AA |ESYGKINPELVCCNPHHLSRLCELESPPPPYSRYPMDFLKPTADCPDAVPSSAETGGTNY| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....25...,....26...,....27...,....28...,....29...,....30 AA |LAPGGLSDSQLLLEPGDRSHWCVVAYWEEKTRVGRLYCVQEPSLDIFYDLPQGNGFCLGQ| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....31...,....32...,....33...,....34...,....35...,....36 AA |LNSDNKSQLVQKVRSKIGCGIQLTREVDGVWVYNRSSYPIFIKSATLDNPDSRTLLVHKV| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....37...,....38...,....39...,....40...,....41...,....42 AA |FPGFSIKAFDYEKAYSLQRPNDHEFMQQPWTGFTVQISFVKGWGQCYTRQFISSCPCWLE| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....43...,....44...,....45...,....46...,....47...,....48 AA |VIFNSR| PHD htm | | detail: prH htm |000000| prL htm |999999| subset: SUB htm |......| --- --- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END ---