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Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions
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| Zeitschriftentitel: | Proteins: Structure, Function, and Bioinformatics |
|---|---|
| Personen und Körperschaften: | , |
| In: | Proteins: Structure, Function, and Bioinformatics, 74, 2009, 2, S. 353-367 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
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| Schlagwörter: |
| author_facet |
Koch, Oliver Klebe, Gerhard Koch, Oliver Klebe, Gerhard |
|---|---|
| author |
Koch, Oliver Klebe, Gerhard |
| spellingShingle |
Koch, Oliver Klebe, Gerhard Proteins: Structure, Function, and Bioinformatics Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions Molecular Biology Biochemistry Structural Biology |
| author_sort |
koch, oliver |
| spelling |
Koch, Oliver Klebe, Gerhard 0887-3585 1097-0134 Wiley Molecular Biology Biochemistry Structural Biology http://dx.doi.org/10.1002/prot.22185 <jats:title>Abstract</jats:title><jats:p>Turns are irregular secondary structure elements with a hydrogen bond or a specific Cα‐Cα distance between the first and the last residue. They are up to six residues in length. Here, we present a uniform classification for all normal (CO<jats:sub>i</jats:sub> – NH<jats:sub>i+n</jats:sub> hydrogen bond), open (a Cα<jats:sub>i</jats:sub>‐Cα<jats:sub>i+n</jats:sub> distance up to 10 Å), and reverse (NH<jats:sub>i</jats:sub> – CO<jats:sub>i+i</jats:sub> hydrogen bond) turn families based on current structural data. Considering the large amount of data evaluated, this classification likely covers quite comprehensively most of the possible conformations of turns. All turn structures of a nonredundant dataset of 1903 protein chains were retrieved using Relibase and clustered using emergent self‐organizing maps. This leads to three normal, four open, and five reverse turn families with several new turn‐types. Based on the amino acid propensities, the achieved separation into normal, open, and reverse turn families seems convincing. In combination with β‐sheet and helix classification on average 96% of the given protein chain can now be successfully classified. Proteins 2009. © 2008 Wiley‐Liss, Inc.</jats:p> Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions Proteins: Structure, Function, and Bioinformatics |
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Proteins: Structure, Function, and Bioinformatics |
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| title |
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_unstemmed |
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_full |
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_fullStr |
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_full_unstemmed |
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_short |
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_sort |
turns revisited: a uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| topic |
Molecular Biology Biochemistry Structural Biology |
| url |
http://dx.doi.org/10.1002/prot.22185 |
| publishDate |
2009 |
| physical |
353-367 |
| description |
<jats:title>Abstract</jats:title><jats:p>Turns are irregular secondary structure elements with a hydrogen bond or a specific Cα‐Cα distance between the first and the last residue. They are up to six residues in length. Here, we present a uniform classification for all normal (CO<jats:sub>i</jats:sub> – NH<jats:sub>i+n</jats:sub> hydrogen bond), open (a Cα<jats:sub>i</jats:sub>‐Cα<jats:sub>i+n</jats:sub> distance up to 10 Å), and reverse (NH<jats:sub>i</jats:sub> – CO<jats:sub>i+i</jats:sub> hydrogen bond) turn families based on current structural data. Considering the large amount of data evaluated, this classification likely covers quite comprehensively most of the possible conformations of turns. All turn structures of a nonredundant dataset of 1903 protein chains were retrieved using Relibase and clustered using emergent self‐organizing maps. This leads to three normal, four open, and five reverse turn families with several new turn‐types. Based on the amino acid propensities, the achieved separation into normal, open, and reverse turn families seems convincing. In combination with β‐sheet and helix classification on average 96% of the given protein chain can now be successfully classified. Proteins 2009. © 2008 Wiley‐Liss, Inc.</jats:p> |
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| description | <jats:title>Abstract</jats:title><jats:p>Turns are irregular secondary structure elements with a hydrogen bond or a specific Cα‐Cα distance between the first and the last residue. They are up to six residues in length. Here, we present a uniform classification for all normal (CO<jats:sub>i</jats:sub> – NH<jats:sub>i+n</jats:sub> hydrogen bond), open (a Cα<jats:sub>i</jats:sub>‐Cα<jats:sub>i+n</jats:sub> distance up to 10 Å), and reverse (NH<jats:sub>i</jats:sub> – CO<jats:sub>i+i</jats:sub> hydrogen bond) turn families based on current structural data. Considering the large amount of data evaluated, this classification likely covers quite comprehensively most of the possible conformations of turns. All turn structures of a nonredundant dataset of 1903 protein chains were retrieved using Relibase and clustered using emergent self‐organizing maps. This leads to three normal, four open, and five reverse turn families with several new turn‐types. Based on the amino acid propensities, the achieved separation into normal, open, and reverse turn families seems convincing. In combination with β‐sheet and helix classification on average 96% of the given protein chain can now be successfully classified. Proteins 2009. © 2008 Wiley‐Liss, Inc.</jats:p> |
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| spelling | Koch, Oliver Klebe, Gerhard 0887-3585 1097-0134 Wiley Molecular Biology Biochemistry Structural Biology http://dx.doi.org/10.1002/prot.22185 <jats:title>Abstract</jats:title><jats:p>Turns are irregular secondary structure elements with a hydrogen bond or a specific Cα‐Cα distance between the first and the last residue. They are up to six residues in length. Here, we present a uniform classification for all normal (CO<jats:sub>i</jats:sub> – NH<jats:sub>i+n</jats:sub> hydrogen bond), open (a Cα<jats:sub>i</jats:sub>‐Cα<jats:sub>i+n</jats:sub> distance up to 10 Å), and reverse (NH<jats:sub>i</jats:sub> – CO<jats:sub>i+i</jats:sub> hydrogen bond) turn families based on current structural data. Considering the large amount of data evaluated, this classification likely covers quite comprehensively most of the possible conformations of turns. All turn structures of a nonredundant dataset of 1903 protein chains were retrieved using Relibase and clustered using emergent self‐organizing maps. This leads to three normal, four open, and five reverse turn families with several new turn‐types. Based on the amino acid propensities, the achieved separation into normal, open, and reverse turn families seems convincing. In combination with β‐sheet and helix classification on average 96% of the given protein chain can now be successfully classified. Proteins 2009. © 2008 Wiley‐Liss, Inc.</jats:p> Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions Proteins: Structure, Function, and Bioinformatics |
| spellingShingle | Koch, Oliver, Klebe, Gerhard, Proteins: Structure, Function, and Bioinformatics, Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions, Molecular Biology, Biochemistry, Structural Biology |
| title | Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_full | Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_fullStr | Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_full_unstemmed | Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_short | Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_sort | turns revisited: a uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| title_unstemmed | Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions |
| topic | Molecular Biology, Biochemistry, Structural Biology |
| url | http://dx.doi.org/10.1002/prot.22185 |