CSS-Palm 2.0: an updated software for palmitoylation sites prediction
Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoyla...
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| Published in | Protein engineering, design and selection Vol. 21; no. 11; pp. 639 - 644 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.11.2008
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1741-0126 1741-0134 1741-0134 |
| DOI | 10.1093/protein/gzn039 |
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| Abstract | Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm. |
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| AbstractList | Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm. Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm . Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm.Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm. |
| Author | Ren, Jian Yao, Xuebiao Wen, Longping Jin, Changjiang Xue, Yu Gao, Xinjiao |
| AuthorAffiliation | 1 Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences , University of Science & Technology of China , Hefei, Anhui 230027 , China |
| AuthorAffiliation_xml | – name: 1 Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences , University of Science & Technology of China , Hefei, Anhui 230027 , China |
| Author_xml | – sequence: 1 givenname: Jian surname: Ren fullname: Ren, Jian organization: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China – sequence: 2 givenname: Longping surname: Wen fullname: Wen, Longping organization: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China – sequence: 3 givenname: Xinjiao surname: Gao fullname: Gao, Xinjiao organization: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China – sequence: 4 givenname: Changjiang surname: Jin fullname: Jin, Changjiang organization: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China – sequence: 5 givenname: Yu surname: Xue fullname: Xue, Yu email: yaoxb@ustc.edu.cn, To whom correspondence should be addressed. yaoxb@ustc.edu.cn (Y.X.)/xueyu@ustc.edu.cn (X.Y.) organization: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China – sequence: 6 givenname: Xuebiao surname: Yao fullname: Yao, Xuebiao email: yaoxb@ustc.edu.cn, To whom correspondence should be addressed. yaoxb@ustc.edu.cn (Y.X.)/xueyu@ustc.edu.cn (X.Y.) organization: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/18753194$$D View this record in MEDLINE/PubMed |
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| Title | CSS-Palm 2.0: an updated software for palmitoylation sites prediction |
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