Commit 83528736 authored by waldispuhl's avatar waldispuhl
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minor changes

parent b91390c4
...@@ -422,13 +422,7 @@ The c-di-GMP riboswitch is present in family \texttt{RF01051} in \rfam, which co ...@@ -422,13 +422,7 @@ The c-di-GMP riboswitch is present in family \texttt{RF01051} in \rfam, which co
{\color{red} {\color{red}
The MaM cobalamin riboswitch sequence can be found in the \rfam family \texttt{RF00174} which has $430$ seed sequences. The PDB contains the structure bounded to its ligand (PDB identifier \texttt{4GXY}). Noticeably, the MaM experiments were done in the presence of cobalamin ligands. The MaM cobalamin riboswitch sequence can be found in the \rfam family \texttt{RF00174} which has $430$ seed sequences. The PDB contains the structure bounded to its ligand (PDB identifier \texttt{4GXY}). Noticeably, the MaM experiments were done in the presence of cobalamin ligands.
The adenine riboswitch belongs to family \texttt{RF00167} which has $133$ seed sequences. The structure with the adenine ligand�has PDB identifier \texttt {1Y26}. Three different MaM experiments were conducted on this molecule. Experiments \texttt{Adenine\char`_2} and \texttt{Adenine\char`_3} where done in presence of the ligand, and are used in this paper. The third experiment \texttt{Adenine\char`_4} has been performed in absence of the ligand, and thus was omitted from this benchmark since disruptive mutations cannot be used to detect key structural elements of the ligand-bound structure. Nonetheless, the results are indicated in the supplementary material. The adenine riboswitch belongs to family \texttt{RF00167} which has $133$ seed sequences. The structure with the adenine ligand�has PDB identifier \texttt {1Y26}. Three different MaM experiments were conducted on this molecule. Experiments \texttt{Adenine\char`_2} and \texttt{Adenine\char`_3} where done in presence of the ligand, and are used in this paper. The third experiment \texttt{Adenine\char`_4} has been performed in absence of the ligand, and thus was omitted from this benchmark since disruptive mutations cannot be used to detect key structural elements of the ligand-bound structure. Nonetheless, the results are indicated in the supplementary material.}
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{\color{red} To complete our benchmark, we also built a secondary test set of \rfam families with experimentally determined 3D structures, but for which MaM experiments were not available.} We selected all \rfam families with sequences having a size ranging from 35 to 150 nucleotides, and with PDB files containing at least one other molecule in the vicinity of the RNA. In total, we found 14 families matching 729 different structures. {\color{red} To complete our benchmark, we also built a secondary test set of \rfam families with experimentally determined 3D structures, but for which MaM experiments were not available.} We selected all \rfam families with sequences having a size ranging from 35 to 150 nucleotides, and with PDB files containing at least one other molecule in the vicinity of the RNA. In total, we found 14 families matching 729 different structures.
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