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How to cite

RNA fragment assembly with experimental restraints
Grzegorz Chojnowski, Rafał Zaborowski, Marcin Magnus, and Janusz M. Bujnicki
submitted

Third party methods

RNAMasonry depends on a number of third-party tools. We are very grateful to their authors for making the software freely available. Please consider citing relevant publications from the list below.

Scoring function

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM NAR 2015, [doi: 10.1093/nar/gkv1479]

RNA model editing

ModeRNA: a tool for comparative modeling of RNA 3D structure.
Rother M, Rother K, Puton T, Bujnicki JM. Bioinformatics 2011, [doi: 10.1093/bioinformatics/btr400]

2D structure assignment

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes Tomasz Waleń, Grzegorz Chojnowski, Przemysław Gierski, Janusz M. Bujnicki NAR 2014, [doi: 10.1093/nar/gku765]

SAXS restraints

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles Schneidman-Duhovny D, Hammel M, Tainer JA, and Sali A. NAR 2016, [doi: 10.1093/nar/gkw389]

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates Svergun D.I., Barberato C. and Koch M.H.J. J. Appl. Cryst. 1995, 28, 768-773. [doi: 10.1107/S0021889895007047]


International Institute of Molecular and Cell Biology
Laboratory of Bioinformatics and Protein Engineering
Trojdena 4, 02-109 Warsaw, POLAND
tel: +48-22 597 0750
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Laboratory of Bioinformatics and Protein Engineering
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