About: Nucleic acid structure prediction

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Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known).

Attributes	Values
rdf:type	software
rdfs:label	Nucleic acid structure prediction (en) Предсказание вторичной структуры РНК (ru)
rdfs:comment	Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). (en) Предсказа́ние втори́чной структу́ры РНК — метод определения вторичной структуры нуклеиновой кислоты по последовательности её нуклеотидов. Вторичную структуру можно предсказывать для единичной последовательности или анализировать множественное выравнивание семейства родственных РНК. (ru)
foaf:depiction
dcterms:subject	RNA
Wikipage page ID	5054738 (xsd:integer)
Wikipage revision ID	1112933619 (xsd:integer)
Link from a Wikipage to another Wikipage	MicroRNA Methods in Molecular Biology Boltzmann Hydrogen bond Riboswitch In vivo Nucleic acid thermodynamics Nussinov algorithm Pseudoknot Complementarity (molecular biology) Mathematical optimization Transfer RNA Mutual information NP-complete Thermodynamic free energy Stochastic context-free grammar Comparison of nucleic acid simulation software Comparison of software for molecular mechanics modeling Stemloc Dynamic programming Evolution Base pair List of RNA structure prediction software Thermodynamics RNA RNA Stem-loop Heuristic (computer science) Homology (biology) Hoogsteen base pair Double helix Boltzmann distribution Multiple sequence alignment Ribosome Ruth Nussinov Nucleic acid structure Non-coding RNA Spliceosome Base stacking Watson-Crick base pair Secondary structure RNA structure RNA tertiary structure
Link from a Wikipage to an external page	https://zenodo.org/record/1259135%7Cjournal= https://semanticscholar.org/paper/2a37e40d53eb79e0543c2b031b44a4f0cf2e4234%7Cjournal= https://semanticscholar.org/paper/4f3d0ca48fbb587a0aa57b1fd2e51e99f54d9f74 http://ubdata.univie.ac.at/AC12083577 https://web.archive.org/web/20120707173044/http:/genesilico.pl/moderna/
sameAs	Nucleic acid structure prediction Nucleic acid structure prediction Nucleic acid structure prediction Nucleic acid structure prediction Nucleic acid structure prediction Nucleic acid structure prediction
dbp:wikiPageUsesTemplate	dbt:About dbt:Cite_book dbt:Cite_journal dbt:Cleanup_bare_URLs dbt:Reflist dbt:Short_description dbt:Biomolecular_structure
thumbnail	wiki-commons:Special:FilePath/TRNA_structure_space.png?width=300
has abstract	Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). The problem of predicting nucleic acid secondary structure is dependent mainly on base pairing and base stacking interactions; many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. Many secondary structure prediction methods rely on variations of dynamic programming and therefore are unable to efficiently identify pseudoknots. While the methods are similar, there are slight differences in the approaches to RNA and DNA structure prediction. In vivo, DNA structures are more likely to be duplexes with full complementarity between two strands, while RNA structures are more likely to fold into complex secondary and tertiary structures such as in the ribosome, spliceosome, or transfer RNA. This is partly because the extra oxygen in RNA increases the propensity for hydrogen bonding in the nucleic acid backbone. The energy parameters are also different for the two nucleic acids. The structure prediction methods can follow a completely theoretical approach, or a hybrid one incorporating experimental data. (en) Предсказа́ние втори́чной структу́ры РНК — метод определения вторичной структуры нуклеиновой кислоты по последовательности её нуклеотидов. Вторичную структуру можно предсказывать для единичной последовательности или анализировать множественное выравнивание семейства родственных РНК. Вторичная структура нуклеиновой кислоты зависит, главным образом, от спаривания оснований друг с другом и стэкинг-взаимодействий. Однако во многих случаях вторичная структура РНК сохраняется в ходе эволюции в большей степени, чем её первичная последовательность. Многие способы предсказания вторичной структуры основаны на методе динамического программирования и не в состоянии эффективно выявлять псевдоузлы. Несмотря на схожесть, существуют некоторые различия в методах предсказания структур ДНК и РНК. В естественных условиях ДНК чаще всего представляет собой полностью комплементарный дуплекс, в то время как РНК образует сложные вторичные и третичные структуры, как, например, у тРНК, рибосомальных РНК или сплайсосом. Происходит это отчасти потому, что дополнительный атом кислорода в составе рибозы увеличивает склонность к образованию водородной связи основной цепью нуклеиновой кислоты. Отличаются и энергетические параметры двух этих нуклеиновых кислот. (ru)
gold:hypernym	Method
prov:wasDerivedFrom	wikipedia-en:Nucleic_acid_structure_prediction?oldid=1112933619&ns=0
page length (characters) of wiki page	34673 (xsd:nonNegativeInteger)
foaf:isPrimaryTopicOf	wikipedia-en:Nucleic_acid_structure_prediction
is Link from a Wikipage to another Wikipage of	List of computational chemists Robert Dirks ViennaRNA Package Influenza A segment 7 splice site Nucleic acid design Nucleic acid secondary structure Nucleic acid structure determination Nussinov algorithm Pseudoknot Nucleic acid tertiary structure NUPACK Anti-hemB RNA motif Comparison of nucleic acid simulation software Gamma-150 RNA motif Biomolecular structure TD-1 RNA motif TD-2 RNA motif Olke C. Uhlenbeck Secondary structure prediction Ruth Nussinov Nucleic acid structure RNA structure prediction

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