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On this point some remarks are necessary. For each pfam domain selected:  \begin{itemize}  \item We collect all PDB with a biological assembly that contains homo-oligomers of the pfam domain selected.  \item For each PDB we take into account repetition of the domain inside the same chain and different biological assemblies annotated. At the end one homo-oligomer pairing are identified unambiguously by pfam ID, PDB ID, chain identifier 1, chain identifier 2, chain 1 domain number,chain 2 domain number, biological assembly identifier.  \item  We create a map between the alignment positions and the 3D inter-residues real positions distances  for each PDB ( \textbf{backmapping} ) To do so we extract the real positions minimal distances  between residues: the heavy atoms between residues in the domain:  \begin{enumerate}  \item within the domains on the different chains, i.e. the \textit{intra-chains distances},   \item between different chains (paired domains in different homo-oligomers), i.e. the \textit{inter-chains distances}. \end{enumerate}  \item We select only chains that have a given coverage of the domain, backmapped part of the domain over $ 60 \% $.   \item In order to include only interacting homo-oligomers we filter out the ones that have an interaction surface under a given threshold.  \item   \end{itemize}  At the final step we have TOT pfam domains with TOT PDB for a total of TOT inter-chains tables and TOT intra-chains tables.  To compare the DCA results with the inter-distance and the intra-distance, we take for each pfam the minimal distance across the PDB,chains,assembly individual distances, for both the intra-distances and the inter-distances.   In the last case the distance matrix are not symmetric, dist(res1,res2) $\neq$ dist(res2,res1). To superimpose the single distance matrices, in principle one can perform a structure alignment of the chain-chain complex but for different assemblies can be ambiguous. We decide then to symmetrize the matrix taking the minimum distance between the distances in the two direction (min(dist(res1,res2),dist(res2,res1))).  \section{Preliminary Results} 
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