Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm.
The present article introduces a set of novel methods that facilitate the use of "natural moves" or arbitrary degrees of freedom that can give rise to collective rearrangements in the structure of biological macromolecules. While such "natural moves" may spoil the stereochemistry...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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2010
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| _version_ | 1826262045103751168 |
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| author | Minary, P Levitt, M |
| author_facet | Minary, P Levitt, M |
| author_sort | Minary, P |
| collection | OXFORD |
| description | The present article introduces a set of novel methods that facilitate the use of "natural moves" or arbitrary degrees of freedom that can give rise to collective rearrangements in the structure of biological macromolecules. While such "natural moves" may spoil the stereochemistry and even break the bonded chain at multiple locations, our new method restores the correct chain geometry by adjusting bond and torsion angles in an arbitrary defined molten zone. This is done by successive stages of partial closure that propagate the location of the chain break backwards along the chain. At the end of these stages, the size of the chain break is generally reduced so much that it can be repaired by adjusting the position of a single atom. Our chain closure method is efficient with a computational complexity of O(N(d)), where N(d) is the number of degrees of freedom used to repair the chain break. The new method facilitates the use of arbitrary degrees of freedom including the "natural" degrees of freedom inferred from analyzing experimental (X-ray crystallography and nuclear magnetic resonance [NMR]) structures of nucleic acids and proteins. In terms of its ability to generate large conformational moves and its effectiveness in locating low energy states, the new method is robust and computationally efficient. |
| first_indexed | 2024-03-06T19:30:09Z |
| format | Journal article |
| id | oxford-uuid:1d2cce15-6c28-4478-b578-01146ba69fff |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T19:30:09Z |
| publishDate | 2010 |
| record_format | dspace |
| spelling | oxford-uuid:1d2cce15-6c28-4478-b578-01146ba69fff2022-03-26T11:09:27ZConformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:1d2cce15-6c28-4478-b578-01146ba69fffEnglishSymplectic Elements at Oxford2010Minary, PLevitt, MThe present article introduces a set of novel methods that facilitate the use of "natural moves" or arbitrary degrees of freedom that can give rise to collective rearrangements in the structure of biological macromolecules. While such "natural moves" may spoil the stereochemistry and even break the bonded chain at multiple locations, our new method restores the correct chain geometry by adjusting bond and torsion angles in an arbitrary defined molten zone. This is done by successive stages of partial closure that propagate the location of the chain break backwards along the chain. At the end of these stages, the size of the chain break is generally reduced so much that it can be repaired by adjusting the position of a single atom. Our chain closure method is efficient with a computational complexity of O(N(d)), where N(d) is the number of degrees of freedom used to repair the chain break. The new method facilitates the use of arbitrary degrees of freedom including the "natural" degrees of freedom inferred from analyzing experimental (X-ray crystallography and nuclear magnetic resonance [NMR]) structures of nucleic acids and proteins. In terms of its ability to generate large conformational moves and its effectiveness in locating low energy states, the new method is robust and computationally efficient. |
| spellingShingle | Minary, P Levitt, M Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. |
| title | Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. |
| title_full | Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. |
| title_fullStr | Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. |
| title_full_unstemmed | Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. |
| title_short | Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. |
| title_sort | conformational optimization with natural degrees of freedom a novel stochastic chain closure algorithm |
| work_keys_str_mv | AT minaryp conformationaloptimizationwithnaturaldegreesoffreedomanovelstochasticchainclosurealgorithm AT levittm conformationaloptimizationwithnaturaldegreesoffreedomanovelstochasticchainclosurealgorithm |