Source:http://linkedlifedata.com/resource/pubmed/id/21455962
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
9
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| pubmed:dateCreated |
2011-4-26
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| pubmed:abstractText |
Even a relatively small molecule with 10-20 atoms might have a few local minima, which correspond to different conformers. The number of local minima quickly increases with molecular size and the most common algorithms, driven by calculated forces, frequently identify a minimum, which is closest to the initial structure, rather than the most stable conformer. Here we discuss how to perform a systematic search of the conformational space for a chain-like molecule. Our approach is fully automated and a user has control which chemical bonds will be probed and with which increments. Moreover, whole fragments of the molecule, which are adjacent to each selected rotational bond, are rotated in a properly selected cylindrical coordinate system and unchemical hybridizations and some "clashes" between neighboring groups, which are common when standard Z-matrices are used, are avoided. A library of potentially relevant conformers is created with a tool, which we call SSC, denoting Systematic Screening of Conformers. Each member of the library is prescreened at a predefined level of theory and the most promising conformers are identified. Finally, they are further evaluated at a higher level of theory to identify the most stable structures and their physicochemical properties. As an example, we demonstrate the results of this approach for 2'-deoxycytidine.
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| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:citationSubset |
IM
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| pubmed:chemical | |
| pubmed:status |
MEDLINE
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| pubmed:month |
Jul
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| pubmed:issn |
1096-987X
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| pubmed:author | |
| pubmed:copyrightInfo |
Copyright © 2011 Wiley Periodicals, Inc.
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| pubmed:issnType |
Electronic
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| pubmed:day |
15
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| pubmed:volume |
32
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
2047-54
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| pubmed:meshHeading | |
| pubmed:year |
2011
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| pubmed:articleTitle |
SSC: a tool for constructing libraries for systematic screening of conformers.
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| pubmed:affiliation |
Chemistry--School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom. s.ling@hw.ac.uk
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| pubmed:publicationType |
Journal Article
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