How to cite

RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints
Grzegorz Chojnowski, Rafał Zaborowski, Marcin Magnus, Sunandan Mukherjee, and Janusz M. Bujnicki
doi: Bioinformatics, 2023, btad527

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.

RNA fragments

RNA Bricks—a database of RNA 3D motifs and their interactions
Chojnowski G, Waleń T, Bujnicki JM NAR 2014, [doi: 10.1093/nar/gkt1084]
http://iimcb.genesilico.pl/rnabricks2

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]

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