Valid and invalid implementations of GOR secondary structure predictions
GOR algorithms have long been a standard methodology for predicting protein secondary structure from primary sequence. We have developed two short validation sequences for the GORI and GORII algorithms. Use of these sequences with seven commercial and non-commercial implementations of these algorith...
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| Veröffentlicht in: | Bioinformatics 1994-06, Vol.10 (3), p.341-348 |
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| container_title | Bioinformatics |
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| creator | Ellis, L.B.M Milius, R.P |
| description | GOR algorithms have long been a standard methodology for predicting protein secondary structure from primary sequence. We have developed two short validation sequences for the GORI and GORII algorithms. Use of these sequences with seven commercial and non-commercial implementations of these algorithms demonstrated that several were incorrect implementations, including two of the three commercial modules implementing the GORI algorithm. This may be due to an easy misinterpretation of the GORI algorithm and related data tables. We present the validation sequences and discuss implications of this widely propagated error on secondary and tertiary structure prediction, using several proteins of known structure in three different structural classes as examples. A valid GORI implementation predicts secondary structure increases the accuracy of predictions by from 1-13 percentage points over an invalid implementation based on the easly misinterpretation. A valid implementation of the GORI and GORII algorithms is available from the authors. |
| doi_str_mv | 10.1093/bioinformatics/10.3.341 |
| format | Article |
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We have developed two short validation sequences for the GORI and GORII algorithms. Use of these sequences with seven commercial and non-commercial implementations of these algorithms demonstrated that several were incorrect implementations, including two of the three commercial modules implementing the GORI algorithm. This may be due to an easy misinterpretation of the GORI algorithm and related data tables. We present the validation sequences and discuss implications of this widely propagated error on secondary and tertiary structure prediction, using several proteins of known structure in three different structural classes as examples. A valid GORI implementation predicts secondary structure increases the accuracy of predictions by from 1-13 percentage points over an invalid implementation based on the easly misinterpretation. A valid implementation of the GORI and GORII algorithms is available from the authors.</description><identifier>ISSN: 0266-7061</identifier><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>DOI: 10.1093/bioinformatics/10.3.341</identifier><identifier>PMID: 7922693</identifier><identifier>CODEN: COABER</identifier><language>eng</language><publisher>Washington, DC: Oxford University Press</publisher><subject>Algorithms ; Amino Acid Sequence ; amino acid sequences ; Biological and medical sciences ; Fundamental and applied biological sciences. Psychology ; garnier, osguthorpe, and robson algorithm ; General aspects ; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) ; molecular conformation ; Molecular Sequence Data ; prediction ; Protein Conformation ; protein structure ; Protein Structure, Secondary ; proteins ; Reproducibility of Results ; structure</subject><ispartof>Bioinformatics, 1994-06, Vol.10 (3), p.341-348</ispartof><rights>1994 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=4107276$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/7922693$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ellis, L.B.M</creatorcontrib><creatorcontrib>Milius, R.P</creatorcontrib><title>Valid and invalid implementations of GOR secondary structure predictions</title><title>Bioinformatics</title><addtitle>Comput Appl Biosci</addtitle><description>GOR algorithms have long been a standard methodology for predicting protein secondary structure from primary sequence. We have developed two short validation sequences for the GORI and GORII algorithms. Use of these sequences with seven commercial and non-commercial implementations of these algorithms demonstrated that several were incorrect implementations, including two of the three commercial modules implementing the GORI algorithm. This may be due to an easy misinterpretation of the GORI algorithm and related data tables. We present the validation sequences and discuss implications of this widely propagated error on secondary and tertiary structure prediction, using several proteins of known structure in three different structural classes as examples. A valid GORI implementation predicts secondary structure increases the accuracy of predictions by from 1-13 percentage points over an invalid implementation based on the easly misinterpretation. A valid implementation of the GORI and GORII algorithms is available from the authors.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>amino acid sequences</subject><subject>Biological and medical sciences</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>garnier, osguthorpe, and robson algorithm</subject><subject>General aspects</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</subject><subject>molecular conformation</subject><subject>Molecular Sequence Data</subject><subject>prediction</subject><subject>Protein Conformation</subject><subject>protein structure</subject><subject>Protein Structure, Secondary</subject><subject>proteins</subject><subject>Reproducibility of Results</subject><subject>structure</subject><issn>0266-7061</issn><issn>1367-4803</issn><issn>1460-2059</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1994</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkFtrFEEQhRtR4hr9CZJ5EN8m6XvPPMqiu2JIQKMGX5rqm7TOTK_dM6L_3t7ssuBTFXW-OlUchC4IviS4Z1cmpjiFlEeYoy1XdcwuGSeP0IpwiVuKRf8YrTCVslVYkqfoWSk_MBaEc36GzlRPqezZCm2_wBBdA5Nr4vT7oY_jbvCjn-ZqnabSpNBsbj82xds0Och_mzLnxc5L9s0uexftA_YcPQkwFP_iWM_R3bu3d-tte327eb9-c91axsXcCkJxMDI4UD0znnBjnAJhqAMROmEAjGRd57CVnotAles7LjkAd4ERxs7R64PtLqdfiy-zHmOxfhhg8mkpWknFlOxpBdUBtDmVkn3QuxzH-r4mWO8j1P9HuB8zXSOsmy-PJxYzenfaO2ZW9VdHHYqFIWSYbCwnjBOsqJIVaw9YLLP_c5Ih_9T7H4Xe3n_Tm68fyP1mfaNvKn9x4AMkDd9ztfz8iWLCMOE97YRk_wDCaphO</recordid><startdate>19940601</startdate><enddate>19940601</enddate><creator>Ellis, L.B.M</creator><creator>Milius, R.P</creator><general>Oxford University Press</general><scope>FBQ</scope><scope>BSCLL</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>19940601</creationdate><title>Valid and invalid implementations of GOR secondary structure predictions</title><author>Ellis, L.B.M ; Milius, R.P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c345t-5120fb6fda793be14bbd7a5b2da5f85baab6388d0c6e45f27d98464aa4df3133</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1994</creationdate><topic>Algorithms</topic><topic>Amino Acid Sequence</topic><topic>amino acid sequences</topic><topic>Biological and medical sciences</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>garnier, osguthorpe, and robson algorithm</topic><topic>General aspects</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>molecular conformation</topic><topic>Molecular Sequence Data</topic><topic>prediction</topic><topic>Protein Conformation</topic><topic>protein structure</topic><topic>Protein Structure, Secondary</topic><topic>proteins</topic><topic>Reproducibility of Results</topic><topic>structure</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ellis, L.B.M</creatorcontrib><creatorcontrib>Milius, R.P</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ellis, L.B.M</au><au>Milius, R.P</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Valid and invalid implementations of GOR secondary structure predictions</atitle><jtitle>Bioinformatics</jtitle><addtitle>Comput Appl Biosci</addtitle><date>1994-06-01</date><risdate>1994</risdate><volume>10</volume><issue>3</issue><spage>341</spage><epage>348</epage><pages>341-348</pages><issn>0266-7061</issn><issn>1367-4803</issn><eissn>1460-2059</eissn><coden>COABER</coden><abstract>GOR algorithms have long been a standard methodology for predicting protein secondary structure from primary sequence. We have developed two short validation sequences for the GORI and GORII algorithms. Use of these sequences with seven commercial and non-commercial implementations of these algorithms demonstrated that several were incorrect implementations, including two of the three commercial modules implementing the GORI algorithm. This may be due to an easy misinterpretation of the GORI algorithm and related data tables. We present the validation sequences and discuss implications of this widely propagated error on secondary and tertiary structure prediction, using several proteins of known structure in three different structural classes as examples. A valid GORI implementation predicts secondary structure increases the accuracy of predictions by from 1-13 percentage points over an invalid implementation based on the easly misinterpretation. A valid implementation of the GORI and GORII algorithms is available from the authors.</abstract><cop>Washington, DC</cop><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>7922693</pmid><doi>10.1093/bioinformatics/10.3.341</doi><tpages>8</tpages></addata></record> |
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| identifier | ISSN: 0266-7061 |
| ispartof | Bioinformatics, 1994-06, Vol.10 (3), p.341-348 |
| issn | 0266-7061 1367-4803 1460-2059 |
| language | eng |
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| source | MEDLINE; Oxford University Press Journals Digital Archive Legacy; Oxford Journals Open Access Collection; Alma/SFX Local Collection |
| subjects | Algorithms Amino Acid Sequence amino acid sequences Biological and medical sciences Fundamental and applied biological sciences. Psychology garnier, osguthorpe, and robson algorithm General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) molecular conformation Molecular Sequence Data prediction Protein Conformation protein structure Protein Structure, Secondary proteins Reproducibility of Results structure |
| title | Valid and invalid implementations of GOR secondary structure predictions |
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