Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index
<p>Abstract</p> <p>Background</p> <p>Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an es...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2006-12-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://dx.doi.org/10.1186/1471-2105-7-S5-S6 |
| _version_ | 1811286930883608576 |
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| author | Zomaya Albert Y Sikder Abdur R |
| author_facet | Zomaya Albert Y Sikder Abdur R |
| author_sort | Zomaya Albert Y |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an essential step in many types of protein analyses. In this present study, we demonstrate that the performance of DomainDiscovery is improved significantly by including the inter-domain linker index value for domain identification from sequence-based information. Improved DomainDiscovery uses a Support Vector Machine (SVM) approach and a unique training dataset built on the principle of consensus among experts in defining domains in protein structure. The SVM was trained using a PSSM (Position Specific Scoring Matrix), secondary structure, solvent accessibility information and inter-domain linker index to detect possible domain boundaries for a target sequence.</p> <p>Results</p> <p>Improved DomainDiscovery is compared with other methods by benchmarking against a structurally non-redundant dataset and also CASP5 targets. Improved DomainDiscovery achieves 70% accuracy for domain boundary identification in multi-domains proteins.</p> <p>Conclusion</p> <p>Improved DomainDiscovery compares favourably to the performance of other methods and excels in the identification of domain boundaries for multi-domain proteins as a result of introducing support vector machine with benchmark_2 dataset.</p> |
| first_indexed | 2024-04-13T03:09:47Z |
| format | Article |
| id | doaj.art-6ce5b7376fb64467b105dd5f405fae70 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T03:09:47Z |
| publishDate | 2006-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-6ce5b7376fb64467b105dd5f405fae702022-12-22T03:05:07ZengBMCBMC Bioinformatics1471-21052006-12-017Suppl 5S610.1186/1471-2105-7-S5-S6Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker indexZomaya Albert YSikder Abdur R<p>Abstract</p> <p>Background</p> <p>Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an essential step in many types of protein analyses. In this present study, we demonstrate that the performance of DomainDiscovery is improved significantly by including the inter-domain linker index value for domain identification from sequence-based information. Improved DomainDiscovery uses a Support Vector Machine (SVM) approach and a unique training dataset built on the principle of consensus among experts in defining domains in protein structure. The SVM was trained using a PSSM (Position Specific Scoring Matrix), secondary structure, solvent accessibility information and inter-domain linker index to detect possible domain boundaries for a target sequence.</p> <p>Results</p> <p>Improved DomainDiscovery is compared with other methods by benchmarking against a structurally non-redundant dataset and also CASP5 targets. Improved DomainDiscovery achieves 70% accuracy for domain boundary identification in multi-domains proteins.</p> <p>Conclusion</p> <p>Improved DomainDiscovery compares favourably to the performance of other methods and excels in the identification of domain boundaries for multi-domain proteins as a result of introducing support vector machine with benchmark_2 dataset.</p>http://dx.doi.org/10.1186/1471-2105-7-S5-S6 |
| spellingShingle | Zomaya Albert Y Sikder Abdur R Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index BMC Bioinformatics |
| title | Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index |
| title_full | Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index |
| title_fullStr | Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index |
| title_full_unstemmed | Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index |
| title_short | Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index |
| title_sort | improving the performance of domaindiscovery of protein domain boundary assignment using inter domain linker index |
| url | http://dx.doi.org/10.1186/1471-2105-7-S5-S6 |
| work_keys_str_mv | AT zomayaalberty improvingtheperformanceofdomaindiscoveryofproteindomainboundaryassignmentusinginterdomainlinkerindex AT sikderabdurr improvingtheperformanceofdomaindiscoveryofproteindomainboundaryassignmentusinginterdomainlinkerindex |