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Guido Uguzzoni edited untitled.tex
over 8 years ago
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We decide then to symmetrize the matrix taking the minimum distance between the two distances ( min(dist(res1,res2),dist(res2,res1)) ).
The procedure to reduce several PDB contact map to one as the union of the contact maps (minimum distance method) can arise pathological situations. Due to the heterogeneity of the different biological assembly architectures the union contact map can present a contact density very high that can bias the results.\\
This happened also with minor intensity in the intra-chain distances for the intrinsic variability of the domains structure (for example when the structures
sampled sample different conformational states).\\
Otherwise is possible to define a "consensus" contact map, where are considered contacts the pairs of residues that are in contact in at least a given percentage of the structures selected. This procedure require to have sampled in some sense fairly the space of possible structures (a possible procedure is to clusterize all the solved domains complex structures).
In the figure 1,2,3,4 are shown the contact densities for each domains for intra-chain and inter-chain, and the scatter plot with the number of structure unit (domains pairings).\\
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