@@ -388,33 +388,28 @@ The whole implementation is freely available at:
\subsection{Dataset}
To evaluate the efficiency of our method, data with the desired properties was available for {\color{red}six} RNAs~\cite{Cordero:2012aa}. These required properties are a mutate-and-map experiment data set, a determined three-dimensional structures interacting with other chain(s) and and \rfam alignment. Those {\color{red}six} RNAs are the 5S ribosomal RNA, {\color{red}the phenylalanine tRNA, the c-di-GMP riboswitch, the cobalamin riboswitch (Puzzle 6), the adenine riboswitch and the glycine riboswitch . Info see Table~\ref{table:datasetinfo}.}
To evaluate the efficiency of our method, data with the desired properties was available for {\color{red}six} RNAs~\cite{Cordero:2012aa}. These required properties are a mutate-and-map experiment data set, a determined three-dimensional structures interacting with other chain(s) and and \rfam alignment. Those {\color{red}six} RNAs are the 5S ribosomal RNA, {\color{red} the c-di-GMP riboswitch, the cobalamin riboswitch (Puzzle 6), the adenine riboswitch, the phenylalanine tRNA and the glycine riboswitch . }
{\color{red} REF Table SUP MAT FOR ALL BINDING SITES}
{\color{red}The latest gave poor results, potentially due to an artificial hairpin, introduced in the sequence, binding to a small protein to help the crystalisation. The protein was missing in the MaM experiments. It was thus omitted in the present analysis. The results are shown in supplementary material (Fig.~S7).}
\begin{table}[t]
\rotatebox{90}{
\centering
\colorbox{red}{
\begin{tabular}{lllll}
RNA & Binding to & RFAM & PDB(s) &Binding Positions on PDB \\\hline\hline
\multicolumn{1}{l|}{RNA}& Total relative entropy \\\hline
5S &\phantom{0}70.210 \\
c-di-GMP ribo. &\phantom{0}56.898 \\
cobalamin ribo. & 112.690 \\
adenine ribo. &\phantom{0}60.180 \\
tRNA &\phantom{0}56.303 \\
glycine ribo. &\phantom{0}58.410 \\
\end{tabular}
}
}
\caption{{\color{red}For each RNA some info}}
\label{table:datasetinfo}
\caption{{\color{red}Each sequence total relative entropy when aligned to its RFAM sequence, obtained from \texttt{infernal}}}
\label{table:ali_entropy}
\end{table}
The 5S ribosomal RNA is the family \texttt{RF00001} on \rfam. Its seed alignment consist of $713$ sequences. The family also provides the consensus structure. The mutate-and-map protocol was applied to the consensus sequence of $4$ structures which have as PDB identifiers \texttt{2WWQ}~\cite{2WWQ}, \texttt{3OAS} and \texttt{3OFC}~\cite{3OAS_3OFC}, and \texttt{3ORB}~\cite{3ORB}. We present in Fig.~\ref{fig:shape}a, for every position $i$, the value of $\Delta(S, S_i)$, with the aligned \rfam consensus secondary structure below. Those four determined structures have almost the same sequence with slight differences in the length on their $5'$ and $3'$ extremities.
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@@ -528,13 +523,13 @@ structural differences. We present in Fig.~\ref{fig:dist} the distribution of pa
