A tetrapeptide-based method for polyproline II-type secondary structure prediction
We describe a new method for polyproline II‐type (PPII) secondary structure prediction based on tetrapeptide conformation properties using data obtained from all globular proteins in the Protein Data Bank (PDB). This is the first method for PPII prediction with a relatively high level of accuracy (∼...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2005-12, Vol.61 (4), p.763-768 |
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| container_title | Proteins, structure, function, and bioinformatics |
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| creator | Vlasov, Peter K. Vlasova, Anna V. Tumanyan, Vladimir G. Esipova, Natalia G. |
| description | We describe a new method for polyproline II‐type (PPII) secondary structure prediction based on tetrapeptide conformation properties using data obtained from all globular proteins in the Protein Data Bank (PDB). This is the first method for PPII prediction with a relatively high level of accuracy (∼60%). Our method uses only frequencies of different conformations among oligopeptides without any additional parameters. We also attempted to predict α‐helices and β‐strands using the same approach. We find that the application of our method reveals interrelation between sequence and structure even for very short oligopeptides (tetrapeptides). Proteins 2005. © 2005 Wiley‐Liss, Inc. |
| doi_str_mv | 10.1002/prot.20670 |
| format | Article |
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This is the first method for PPII prediction with a relatively high level of accuracy (∼60%). Our method uses only frequencies of different conformations among oligopeptides without any additional parameters. We also attempted to predict α‐helices and β‐strands using the same approach. We find that the application of our method reveals interrelation between sequence and structure even for very short oligopeptides (tetrapeptides). 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Proteins 2005. © 2005 Wiley‐Liss, Inc.</description><subject>Databases, Protein</subject><subject>Models, Molecular</subject><subject>Oligopeptides - chemistry</subject><subject>Peptides - chemistry</subject><subject>polyproline II-type structure</subject><subject>prediction</subject><subject>Protein Conformation</subject><subject>Protein Structure, Secondary</subject><subject>secondary structure</subject><subject>tetrapeptides</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkMtOwzAQRS0EgvLY8AEoKxZIKWO7fmQJFY-KikIFYmkZZyICaRNsR9C_J9ACO1jN5syZO5eQfQp9CsCOG1_HPgOpYI30KGQqBcoH66QHWquUCy22yHYIzwAgMy43yRaVjFNOoUemJ0nE6G2DTSxzTB9twDyZYXyq86SofdLU1aI7UJVzTEajNC4aTAK6ep5bv0hC9K2Lrcek8ZiXLpb1fJdsFLYKuLeaO-T-_OxueJmOJxej4ck4dTyTkLLMWg6MFRqkRgbKZcVgoIVkXXiOktuiyFwOglu0KtdIsaDZQKEE67SwfIccLr1dvNcWQzSzMjisKjvHug1Gas24VOpfsLMKwTLWgUdL0Pk6BI-FaXw56_40FMxn1eazavNVdQcfrKzt4wzzX3TVbQfQJfBWVrj4Q2VuppO7b2m63ClDxPefHetfjFRcCfNwfWGumDg_nY5PzS3_AFpQmPs</recordid><startdate>20051201</startdate><enddate>20051201</enddate><creator>Vlasov, Peter K.</creator><creator>Vlasova, Anna V.</creator><creator>Tumanyan, Vladimir G.</creator><creator>Esipova, Natalia G.</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><scope>BSCLL</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>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20051201</creationdate><title>A tetrapeptide-based method for polyproline II-type secondary structure prediction</title><author>Vlasov, Peter K. ; Vlasova, Anna V. ; Tumanyan, Vladimir G. ; Esipova, Natalia G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3960-29aa3022f8068e207c9f4485621343e63aff9cd053aea7d8e1ef1947e60ac85a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Databases, Protein</topic><topic>Models, Molecular</topic><topic>Oligopeptides - chemistry</topic><topic>Peptides - chemistry</topic><topic>polyproline II-type structure</topic><topic>prediction</topic><topic>Protein Conformation</topic><topic>Protein Structure, Secondary</topic><topic>secondary structure</topic><topic>tetrapeptides</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vlasov, Peter K.</creatorcontrib><creatorcontrib>Vlasova, Anna V.</creatorcontrib><creatorcontrib>Tumanyan, Vladimir G.</creatorcontrib><creatorcontrib>Esipova, Natalia G.</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vlasov, Peter K.</au><au>Vlasova, Anna V.</au><au>Tumanyan, Vladimir G.</au><au>Esipova, Natalia G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A tetrapeptide-based method for polyproline II-type secondary structure prediction</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>2005-12-01</date><risdate>2005</risdate><volume>61</volume><issue>4</issue><spage>763</spage><epage>768</epage><pages>763-768</pages><issn>0887-3585</issn><eissn>1097-0134</eissn><abstract>We describe a new method for polyproline II‐type (PPII) secondary structure prediction based on tetrapeptide conformation properties using data obtained from all globular proteins in the Protein Data Bank (PDB). 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| ispartof | Proteins, structure, function, and bioinformatics, 2005-12, Vol.61 (4), p.763-768 |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Databases, Protein Models, Molecular Oligopeptides - chemistry Peptides - chemistry polyproline II-type structure prediction Protein Conformation Protein Structure, Secondary secondary structure tetrapeptides |
| title | A tetrapeptide-based method for polyproline II-type secondary structure prediction |
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