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Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
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| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , |
| In: | Bioinformatics, 21, 2005, 7, S. 1010-1019 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
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| Schlagwörter: |
| author_facet |
Yuan, Xin Bystroff, Christopher Yuan, Xin Bystroff, Christopher |
|---|---|
| author |
Yuan, Xin Bystroff, Christopher |
| spellingShingle |
Yuan, Xin Bystroff, Christopher Bioinformatics Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| author_sort |
yuan, xin |
| spelling |
Yuan, Xin Bystroff, Christopher 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/bti128 <jats:title>Abstract</jats:title><jats:p>Motivation: Proteins of the same class often share a secondary structure packing arrangement but differ in how the secondary structure units are ordered in the sequence. We find that proteins that share a common core also share local sequence–structure similarities, and these can be exploited to align structures with different topologies. In this study, segments from a library of local sequence–structure alignments were assembled hierarchically, enforcing the compactness and conserved inter-residue contacts but not sequential ordering. Previous structure-based alignment methods often ignore sequence similarity, local structural equivalence and compactness.</jats:p><jats:p>Results: The new program, SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the three-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology, but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.</jats:p><jats:p>Availability: An online topology-independent SCALI structure comparison server is available at http://www.bioinfo.rpi.edu/~bystrc/scali.html</jats:p><jats:p>Contact: bystrc@rpi.edu</jats:p> Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins Bioinformatics |
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Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_unstemmed |
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_full |
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_fullStr |
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_full_unstemmed |
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_short |
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_sort |
non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
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http://dx.doi.org/10.1093/bioinformatics/bti128 |
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2005 |
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1010-1019 |
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<jats:title>Abstract</jats:title><jats:p>Motivation: Proteins of the same class often share a secondary structure packing arrangement but differ in how the secondary structure units are ordered in the sequence. We find that proteins that share a common core also share local sequence–structure similarities, and these can be exploited to align structures with different topologies. In this study, segments from a library of local sequence–structure alignments were assembled hierarchically, enforcing the compactness and conserved inter-residue contacts but not sequential ordering. Previous structure-based alignment methods often ignore sequence similarity, local structural equivalence and compactness.</jats:p><jats:p>Results: The new program, SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the three-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology, but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.</jats:p><jats:p>Availability: An online topology-independent SCALI structure comparison server is available at http://www.bioinfo.rpi.edu/~bystrc/scali.html</jats:p><jats:p>Contact: bystrc@rpi.edu</jats:p> |
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| author | Yuan, Xin, Bystroff, Christopher |
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| description | <jats:title>Abstract</jats:title><jats:p>Motivation: Proteins of the same class often share a secondary structure packing arrangement but differ in how the secondary structure units are ordered in the sequence. We find that proteins that share a common core also share local sequence–structure similarities, and these can be exploited to align structures with different topologies. In this study, segments from a library of local sequence–structure alignments were assembled hierarchically, enforcing the compactness and conserved inter-residue contacts but not sequential ordering. Previous structure-based alignment methods often ignore sequence similarity, local structural equivalence and compactness.</jats:p><jats:p>Results: The new program, SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the three-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology, but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.</jats:p><jats:p>Availability: An online topology-independent SCALI structure comparison server is available at http://www.bioinfo.rpi.edu/~bystrc/scali.html</jats:p><jats:p>Contact: bystrc@rpi.edu</jats:p> |
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| spelling | Yuan, Xin Bystroff, Christopher 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/bti128 <jats:title>Abstract</jats:title><jats:p>Motivation: Proteins of the same class often share a secondary structure packing arrangement but differ in how the secondary structure units are ordered in the sequence. We find that proteins that share a common core also share local sequence–structure similarities, and these can be exploited to align structures with different topologies. In this study, segments from a library of local sequence–structure alignments were assembled hierarchically, enforcing the compactness and conserved inter-residue contacts but not sequential ordering. Previous structure-based alignment methods often ignore sequence similarity, local structural equivalence and compactness.</jats:p><jats:p>Results: The new program, SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the three-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology, but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.</jats:p><jats:p>Availability: An online topology-independent SCALI structure comparison server is available at http://www.bioinfo.rpi.edu/~bystrc/scali.html</jats:p><jats:p>Contact: bystrc@rpi.edu</jats:p> Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins Bioinformatics |
| spellingShingle | Yuan, Xin, Bystroff, Christopher, Bioinformatics, Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_full | Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_fullStr | Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_full_unstemmed | Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_short | Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_sort | non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| title_unstemmed | Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/bti128 |