Accurate Fitting SAXS Curves with NMR Structure Ensembles

D 2015

Accurate Fitting SAXS Curves with NMR Structure Ensembles

KŘENEK, Aleš, Karel KUBÍČEK, Richard ŠTEFL a Jiří FILIPOVIČ

Základní údaje

Originální název

Accurate Fitting SAXS Curves with NMR Structure Ensembles

Autoři

KŘENEK, Aleš (203 Česká republika, garant, domácí), Karel KUBÍČEK (203 Česká republika, domácí), Richard ŠTEFL (203 Česká republika, domácí) a Jiří FILIPOVIČ (203 Česká republika, domácí)

Vydání

Pissa, Proceedings of International Symposium on Grids and Clouds 2015, od s. nestránkováno, 9 s. 2015

Nakladatel

Proceedings of Science

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10600 1.6 Biological sciences

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Odkazy

URL

Kód RIV

RIV/00216224:14610/15:00083645

Organizační jednotka

Ústav výpočetní techniky

ISSN

Klíčová slova česky

saxs; nmr; ensamble fit

Klíčová slova anglicky

saxs; nmr; ensamble fit

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 4. 2018 14:31, Mgr. Alena Mokrá

Anotace

V originále

Typical NMR analyses of a biomolecule yields a set of up to few dozens candidate 3D structures of the analyzed molecule without any clues to discriminate among them further. A parallel SAXS experiment on the same sample can be used for this purpose. Previous implementations of “ensemble fit” (search for a mix of molecular conformations which matches the SAXS curve) were designed to choose from a huge ensemble generated by molecular dynamics. Therefore the methods must trade off accuracy for manageable speed, and they end up in mixing curves computed with rather different values of parameters which have physical meaning, which should be avoided. On the contrary, with a relatively small input set of candidate NMR structures we take a more accurate approach. Both the model parameters, considered globally now, and weights of individ- ual candidate structures (reflecting their presence in the solution) become independent variables of a multidimensional global optimization problem; the optimized value is the accuracy of the fit to the experimental data. The optimization must escape from traps of many local minima there- fore we use Monte Carlo with stochastic tunnelling. The method also offers opportunities for parallelization. The final issue is user friendliness of the entire workflow, which is quite complex, involving several programs to be run, handling different file formats, and setting multiple parameters, ending up with visualization of results. We outline design of a web portal hiding these complexities to the end user.

Návaznosti

MUNI/M/1038/2013, interní kód MU

Název: Development of new interdisciplinary approaches to study function and regulation of transcriptome

Investor: Masarykova univerzita, Development of new interdisciplinary approaches to study function and regulation of transcriptome, INTERDISCIPLINARY - Mezioborové výzkumné projekty

Citovat

KŘENEK, Aleš, Karel KUBÍČEK, Richard ŠTEFL a Jiří FILIPOVIČ. Accurate Fitting SAXS Curves with NMR Structure Ensembles. Online. In Simon Lin, Vicky Huang. Proceedings of International Symposium on Grids and Clouds 2015. Pissa: Proceedings of Science, 2015, s. nestránkováno, 9 s. ISSN 1824-8039.

@inproceedings{1309251,
   author = {Křenek, Aleš and Kubíček, Karel and Štefl, Richard and Filipovič, Jiří},
   address = {Pissa},
   booktitle = {Proceedings of International Symposium on Grids and Clouds 2015},
   editor = {Simon Lin, Vicky Huang},
   keywords = {saxs; nmr; ensamble fit},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Pissa},
   pages = {nestránkováno},
   publisher = {Proceedings of Science},
   title = {Accurate Fitting SAXS Curves with NMR Structure Ensembles},
   url = {http://pos.sissa.it/archive/conferences/239/025/ISGC2015_025.pdf},
   year = {2015}
}

TY  - JOUR
ID  - 1309251
AU  - Křenek, Aleš - Kubíček, Karel - Štefl, Richard - Filipovič, Jiří
PY  - 2015
TI  - Accurate Fitting SAXS Curves with NMR Structure Ensembles
PB  - Proceedings of Science
CY  - Pissa
KW  - saxs
KW  - nmr
KW  - ensamble fit
UR  - http://pos.sissa.it/archive/conferences/239/025/ISGC2015_025.pdf
L2  - http://pos.sissa.it/archive/conferences/239/025/ISGC2015_025.pdf
N2  - Typical NMR analyses of a biomolecule yields a set of up to few dozens candidate 3D structures of the analyzed molecule without any clues to discriminate among them further. A parallel SAXS experiment on the same sample can be used for this purpose. Previous implementations of “ensemble fit” (search for a mix of molecular conformations which matches the SAXS curve) were designed to choose from a huge ensemble generated by molecular dynamics. Therefore the methods must trade off accuracy for manageable speed, and they end up in mixing curves computed with rather different values of parameters which have physical meaning, which should be avoided. On the contrary, with a relatively small input set of candidate NMR structures we take a more accurate approach. Both the model parameters, considered globally now, and weights of individ- ual candidate structures (reflecting their presence in the solution) become independent variables of a multidimensional global optimization problem; the optimized value is the accuracy of the fit to the experimental data. The optimization must escape from traps of many local minima there- fore we use Monte Carlo with stochastic tunnelling. The method also offers opportunities for parallelization. The final issue is user friendliness of the entire workflow, which is quite complex, involving several programs to be run, handling different file formats, and setting multiple parameters, ending up with visualization of results. We outline design of a web portal hiding these complexities to the end user.
ER  -

KŘENEK, Aleš, Karel KUBÍČEK, Richard ŠTEFL a Jiří FILIPOVIČ. Accurate Fitting SAXS Curves with NMR Structure Ensembles. Online. In Simon Lin, Vicky Huang. \textit{Proceedings of International Symposium on Grids and Clouds 2015}. Pissa: Proceedings of Science, 2015, s.~nestránkováno, 9 s. ISSN~1824-8039.

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