De novo protein structure prediction using ultra-fast molecular dynamics simulation.
Modern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein struct...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC6245515?pdf=render |
| _version_ | 1819096266707042304 |
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| author | Ngaam J Cheung Wookyung Yu |
| author_facet | Ngaam J Cheung Wookyung Yu |
| author_sort | Ngaam J Cheung |
| collection | DOAJ |
| description | Modern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein structure prediction than ever. Here, we present a system of de novo predictor, termed NiDelta, building on a deep convolutional neural network and statistical potential enabling molecular dynamics simulation for modeling protein tertiary structure. Combining with evolutionary-based residue-contacts, the presented predictor can predict the tertiary structures of a number of target proteins with remarkable accuracy. The proposed approach is demonstrated by calculations on a set of eighteen large proteins from different fold classes. The results show that the ultra-fast molecular dynamics simulation could dramatically reduce the gap between the sequence and its structure at atom level, and it could also present high efficiency in protein structure determination if sparse experimental data is available. |
| first_indexed | 2024-12-21T23:56:28Z |
| format | Article |
| id | doaj.art-340e854ba30448e2ba2df322ab6ba1b2 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T23:56:28Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-340e854ba30448e2ba2df322ab6ba1b22022-12-21T18:45:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-011311e020581910.1371/journal.pone.0205819De novo protein structure prediction using ultra-fast molecular dynamics simulation.Ngaam J CheungWookyung YuModern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein structure prediction than ever. Here, we present a system of de novo predictor, termed NiDelta, building on a deep convolutional neural network and statistical potential enabling molecular dynamics simulation for modeling protein tertiary structure. Combining with evolutionary-based residue-contacts, the presented predictor can predict the tertiary structures of a number of target proteins with remarkable accuracy. The proposed approach is demonstrated by calculations on a set of eighteen large proteins from different fold classes. The results show that the ultra-fast molecular dynamics simulation could dramatically reduce the gap between the sequence and its structure at atom level, and it could also present high efficiency in protein structure determination if sparse experimental data is available.http://europepmc.org/articles/PMC6245515?pdf=render |
| spellingShingle | Ngaam J Cheung Wookyung Yu De novo protein structure prediction using ultra-fast molecular dynamics simulation. PLoS ONE |
| title | De novo protein structure prediction using ultra-fast molecular dynamics simulation. |
| title_full | De novo protein structure prediction using ultra-fast molecular dynamics simulation. |
| title_fullStr | De novo protein structure prediction using ultra-fast molecular dynamics simulation. |
| title_full_unstemmed | De novo protein structure prediction using ultra-fast molecular dynamics simulation. |
| title_short | De novo protein structure prediction using ultra-fast molecular dynamics simulation. |
| title_sort | de novo protein structure prediction using ultra fast molecular dynamics simulation |
| url | http://europepmc.org/articles/PMC6245515?pdf=render |
| work_keys_str_mv | AT ngaamjcheung denovoproteinstructurepredictionusingultrafastmoleculardynamicssimulation AT wookyungyu denovoproteinstructurepredictionusingultrafastmoleculardynamicssimulation |