DNA-binding residues and binding mode prediction with binding-mechanism concerned models
<p>Abstract</p> <p>Background</p> <p>Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into two categories of bindin...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-12-01
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| Series: | BMC Genomics |
| _version_ | 1829471588851908608 |
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| author | Oyang Yen-Jen Liu Yu-Cheng Huang Chun-Chin Huang Yu-Feng Huang Chien-Kang |
| author_facet | Oyang Yen-Jen Liu Yu-Cheng Huang Chun-Chin Huang Yu-Feng Huang Chien-Kang |
| author_sort | Oyang Yen-Jen |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into two categories of binding mechanisms - sequence-specific and non-specific binding. Protein-DNA specific binding provides a mechanism to recognize correct nucleotide base pairs for sequence-specific identification. Protein-DNA non-specific binding shows sequence independent interaction for accelerated targeting by interacting with DNA backbone. Both sequence-specific and non-specific binding residues contribute to their roles for interaction.</p> <p>Results</p> <p>The proposed framework has two stage predictors: DNA-binding residues prediction and binding mode prediction. In the first stage - DNA-binding residues prediction, the predictor for DNA specific binding residues achieves 96.45% accuracy with 50.14% sensitivity, 99.31% specificity, 81.70% precision, and 62.15% F-measure. The predictor for DNA non-specific binding residues achieves 89.14% accuracy with 53.06% sensitivity, 95.25% specificity, 65.47% precision, and 58.62% F-measure. While combining prediction results of sequence-specific and non-specific binding residues with OR operation, the predictor achieves 89.26% accuracy with 56.86% sensitivity, 95.63% specificity, 71.92% precision, and 63.51% F-measure. In the second stage, protein-DNA binding mode prediction achieves 75.83% accuracy while using support vector machine with multi-class prediction.</p> <p>Conclusion</p> <p>This article presents the design of a sequence based predictor aiming to identify sequence-specific and non-specific binding residues in a transcription factor with DNA binding-mechanism concerned. The protein-DNA binding mode prediction was introduced to help improve DNA-binding residues prediction. In addition, the results of this study will help with the design of binding-mechanism concerned predictors for other families of proteins interacting with DNA.</p> |
| first_indexed | 2024-12-14T01:59:20Z |
| format | Article |
| id | doaj.art-99371e8338bd454baff40d4d2d95fa91 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T01:59:20Z |
| publishDate | 2009-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-99371e8338bd454baff40d4d2d95fa912022-12-21T23:21:04ZengBMCBMC Genomics1471-21642009-12-0110Suppl 3S2310.1186/1471-2164-10-S3-S23DNA-binding residues and binding mode prediction with binding-mechanism concerned modelsOyang Yen-JenLiu Yu-ChengHuang Chun-ChinHuang Yu-FengHuang Chien-Kang<p>Abstract</p> <p>Background</p> <p>Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into two categories of binding mechanisms - sequence-specific and non-specific binding. Protein-DNA specific binding provides a mechanism to recognize correct nucleotide base pairs for sequence-specific identification. Protein-DNA non-specific binding shows sequence independent interaction for accelerated targeting by interacting with DNA backbone. Both sequence-specific and non-specific binding residues contribute to their roles for interaction.</p> <p>Results</p> <p>The proposed framework has two stage predictors: DNA-binding residues prediction and binding mode prediction. In the first stage - DNA-binding residues prediction, the predictor for DNA specific binding residues achieves 96.45% accuracy with 50.14% sensitivity, 99.31% specificity, 81.70% precision, and 62.15% F-measure. The predictor for DNA non-specific binding residues achieves 89.14% accuracy with 53.06% sensitivity, 95.25% specificity, 65.47% precision, and 58.62% F-measure. While combining prediction results of sequence-specific and non-specific binding residues with OR operation, the predictor achieves 89.26% accuracy with 56.86% sensitivity, 95.63% specificity, 71.92% precision, and 63.51% F-measure. In the second stage, protein-DNA binding mode prediction achieves 75.83% accuracy while using support vector machine with multi-class prediction.</p> <p>Conclusion</p> <p>This article presents the design of a sequence based predictor aiming to identify sequence-specific and non-specific binding residues in a transcription factor with DNA binding-mechanism concerned. The protein-DNA binding mode prediction was introduced to help improve DNA-binding residues prediction. In addition, the results of this study will help with the design of binding-mechanism concerned predictors for other families of proteins interacting with DNA.</p> |
| spellingShingle | Oyang Yen-Jen Liu Yu-Cheng Huang Chun-Chin Huang Yu-Feng Huang Chien-Kang DNA-binding residues and binding mode prediction with binding-mechanism concerned models BMC Genomics |
| title | DNA-binding residues and binding mode prediction with binding-mechanism concerned models |
| title_full | DNA-binding residues and binding mode prediction with binding-mechanism concerned models |
| title_fullStr | DNA-binding residues and binding mode prediction with binding-mechanism concerned models |
| title_full_unstemmed | DNA-binding residues and binding mode prediction with binding-mechanism concerned models |
| title_short | DNA-binding residues and binding mode prediction with binding-mechanism concerned models |
| title_sort | dna binding residues and binding mode prediction with binding mechanism concerned models |
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