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Prediction of functional sites by analysis of sequence and structure conservation
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| Zeitschriftentitel: | Protein Science |
|---|---|
| Personen und Körperschaften: | , , |
| In: | Protein Science, 13, 2004, 4, S. 884-892 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
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| Schlagwörter: |
| author_facet |
Panchenko, Anna R. Kondrashov, Fyodor Bryant, Stephen Panchenko, Anna R. Kondrashov, Fyodor Bryant, Stephen |
|---|---|
| author |
Panchenko, Anna R. Kondrashov, Fyodor Bryant, Stephen |
| spellingShingle |
Panchenko, Anna R. Kondrashov, Fyodor Bryant, Stephen Protein Science Prediction of functional sites by analysis of sequence and structure conservation Molecular Biology Biochemistry |
| author_sort |
panchenko, anna r. |
| spelling |
Panchenko, Anna R. Kondrashov, Fyodor Bryant, Stephen 0961-8368 1469-896X Wiley Molecular Biology Biochemistry http://dx.doi.org/10.1110/ps.03465504 <jats:title>Abstract</jats:title><jats:p>We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.</jats:p> Prediction of functional sites by analysis of sequence and structure conservation Protein Science |
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Protein Science |
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| title |
Prediction of functional sites by analysis of sequence and structure conservation |
| title_unstemmed |
Prediction of functional sites by analysis of sequence and structure conservation |
| title_full |
Prediction of functional sites by analysis of sequence and structure conservation |
| title_fullStr |
Prediction of functional sites by analysis of sequence and structure conservation |
| title_full_unstemmed |
Prediction of functional sites by analysis of sequence and structure conservation |
| title_short |
Prediction of functional sites by analysis of sequence and structure conservation |
| title_sort |
prediction of functional sites by analysis of sequence and structure conservation |
| topic |
Molecular Biology Biochemistry |
| url |
http://dx.doi.org/10.1110/ps.03465504 |
| publishDate |
2004 |
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884-892 |
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<jats:title>Abstract</jats:title><jats:p>We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.</jats:p> |
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| author | Panchenko, Anna R., Kondrashov, Fyodor, Bryant, Stephen |
| author_facet | Panchenko, Anna R., Kondrashov, Fyodor, Bryant, Stephen, Panchenko, Anna R., Kondrashov, Fyodor, Bryant, Stephen |
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| description | <jats:title>Abstract</jats:title><jats:p>We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.</jats:p> |
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| institution | DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229, DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15 |
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| series | Protein Science |
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| spelling | Panchenko, Anna R. Kondrashov, Fyodor Bryant, Stephen 0961-8368 1469-896X Wiley Molecular Biology Biochemistry http://dx.doi.org/10.1110/ps.03465504 <jats:title>Abstract</jats:title><jats:p>We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.</jats:p> Prediction of functional sites by analysis of sequence and structure conservation Protein Science |
| spellingShingle | Panchenko, Anna R., Kondrashov, Fyodor, Bryant, Stephen, Protein Science, Prediction of functional sites by analysis of sequence and structure conservation, Molecular Biology, Biochemistry |
| title | Prediction of functional sites by analysis of sequence and structure conservation |
| title_full | Prediction of functional sites by analysis of sequence and structure conservation |
| title_fullStr | Prediction of functional sites by analysis of sequence and structure conservation |
| title_full_unstemmed | Prediction of functional sites by analysis of sequence and structure conservation |
| title_short | Prediction of functional sites by analysis of sequence and structure conservation |
| title_sort | prediction of functional sites by analysis of sequence and structure conservation |
| title_unstemmed | Prediction of functional sites by analysis of sequence and structure conservation |
| topic | Molecular Biology, Biochemistry |
| url | http://dx.doi.org/10.1110/ps.03465504 |