Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm.
Fragment assembly is a powerful method of protein structure prediction that builds protein models from a pool of candidate fragments taken from known structures. Stochastic sampling is subsequently used to refine the models. The structures are first represented as coarse-grained models and then as a...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3723781?pdf=render |
| _version_ | 1828199961712394240 |
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| author | David Simoncini Kam Y J Zhang |
| author_facet | David Simoncini Kam Y J Zhang |
| author_sort | David Simoncini |
| collection | DOAJ |
| description | Fragment assembly is a powerful method of protein structure prediction that builds protein models from a pool of candidate fragments taken from known structures. Stochastic sampling is subsequently used to refine the models. The structures are first represented as coarse-grained models and then as all-atom models for computational efficiency. Many models have to be generated independently due to the stochastic nature of the sampling methods used to search for the global minimum in a complex energy landscape. In this paper we present EdaFold(AA), a fragment-based approach which shares information between the generated models and steers the search towards native-like regions. A distribution over fragments is estimated from a pool of low energy all-atom models. This iteratively-refined distribution is used to guide the selection of fragments during the building of models for subsequent rounds of structure prediction. The use of an estimation of distribution algorithm enabled EdaFold(AA) to reach lower energy levels and to generate a higher percentage of near-native models. [Formula: see text] uses an all-atom energy function and produces models with atomic resolution. We observed an improvement in energy-driven blind selection of models on a benchmark of EdaFold(AA) in comparison with the [Formula: see text] AbInitioRelax protocol. |
| first_indexed | 2024-04-12T11:05:30Z |
| format | Article |
| id | doaj.art-4ec6acbde5fe4d56b6dae532837f4689 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T11:05:30Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-4ec6acbde5fe4d56b6dae532837f46892022-12-22T03:35:47ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6895410.1371/journal.pone.0068954Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm.David SimonciniKam Y J ZhangFragment assembly is a powerful method of protein structure prediction that builds protein models from a pool of candidate fragments taken from known structures. Stochastic sampling is subsequently used to refine the models. The structures are first represented as coarse-grained models and then as all-atom models for computational efficiency. Many models have to be generated independently due to the stochastic nature of the sampling methods used to search for the global minimum in a complex energy landscape. In this paper we present EdaFold(AA), a fragment-based approach which shares information between the generated models and steers the search towards native-like regions. A distribution over fragments is estimated from a pool of low energy all-atom models. This iteratively-refined distribution is used to guide the selection of fragments during the building of models for subsequent rounds of structure prediction. The use of an estimation of distribution algorithm enabled EdaFold(AA) to reach lower energy levels and to generate a higher percentage of near-native models. [Formula: see text] uses an all-atom energy function and produces models with atomic resolution. We observed an improvement in energy-driven blind selection of models on a benchmark of EdaFold(AA) in comparison with the [Formula: see text] AbInitioRelax protocol.http://europepmc.org/articles/PMC3723781?pdf=render |
| spellingShingle | David Simoncini Kam Y J Zhang Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. PLoS ONE |
| title | Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. |
| title_full | Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. |
| title_fullStr | Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. |
| title_full_unstemmed | Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. |
| title_short | Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. |
| title_sort | efficient sampling in fragment based protein structure prediction using an estimation of distribution algorithm |
| url | http://europepmc.org/articles/PMC3723781?pdf=render |
| work_keys_str_mv | AT davidsimoncini efficientsamplinginfragmentbasedproteinstructurepredictionusinganestimationofdistributionalgorithm AT kamyjzhang efficientsamplinginfragmentbasedproteinstructurepredictionusinganestimationofdistributionalgorithm |