Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology.
Many template-based modeling (TBM) methods have been developed over the recent years that allow for protein structure prediction and for the study of structure-function relationships for proteins. One major problem all TBM algorithms face, however, is their unsatisfactory performance when proteins u...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089935&type=printable |
| _version_ | 1826799015948189696 |
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| author | Wentao Dai Tingrui Song Xuan Wang Xiaoyang Jin Lizong Deng Aiping Wu Taijiao Jiang |
| author_facet | Wentao Dai Tingrui Song Xuan Wang Xiaoyang Jin Lizong Deng Aiping Wu Taijiao Jiang |
| author_sort | Wentao Dai |
| collection | DOAJ |
| description | Many template-based modeling (TBM) methods have been developed over the recent years that allow for protein structure prediction and for the study of structure-function relationships for proteins. One major problem all TBM algorithms face, however, is their unsatisfactory performance when proteins under consideration are low-homology. To improve the performance of TBM methods for such targets, a novel model evaluation method was developed here, and named MEFTop. Our novel method focuses on evaluating the topology by using two novel groups of features. These novel features included secondary structure element (SSE) contact information and 3-dimensional topology information. By combining MEFTop algorithm with FR-t5, a threading program developed by our group, we found that this modified TBM program, which was named FR-t5-M, exhibited significant improvements in predictive abilities for low-homology protein targets. We further showed that the MEFTop could be a generalized method to improve threading programs for low-homology protein targets. The softwares (FR-t5-M and MEFTop) are available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/FRt5M/FRt5M.html. |
| first_indexed | 2024-12-11T18:27:51Z |
| format | Article |
| id | doaj.art-67938c6cf2fd41afa6f17484886d1215 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2025-03-17T00:28:22Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj.art-67938c6cf2fd41afa6f17484886d12152025-02-21T05:37:35ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0192e8993510.1371/journal.pone.0089935Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology.Wentao DaiTingrui SongXuan WangXiaoyang JinLizong DengAiping WuTaijiao JiangMany template-based modeling (TBM) methods have been developed over the recent years that allow for protein structure prediction and for the study of structure-function relationships for proteins. One major problem all TBM algorithms face, however, is their unsatisfactory performance when proteins under consideration are low-homology. To improve the performance of TBM methods for such targets, a novel model evaluation method was developed here, and named MEFTop. Our novel method focuses on evaluating the topology by using two novel groups of features. These novel features included secondary structure element (SSE) contact information and 3-dimensional topology information. By combining MEFTop algorithm with FR-t5, a threading program developed by our group, we found that this modified TBM program, which was named FR-t5-M, exhibited significant improvements in predictive abilities for low-homology protein targets. We further showed that the MEFTop could be a generalized method to improve threading programs for low-homology protein targets. The softwares (FR-t5-M and MEFTop) are available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/FRt5M/FRt5M.html.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089935&type=printable |
| spellingShingle | Wentao Dai Tingrui Song Xuan Wang Xiaoyang Jin Lizong Deng Aiping Wu Taijiao Jiang Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. PLoS ONE |
| title | Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. |
| title_full | Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. |
| title_fullStr | Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. |
| title_full_unstemmed | Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. |
| title_short | Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. |
| title_sort | improvement in low homology template based modeling by employing a model evaluation method with focus on topology |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089935&type=printable |
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