Additional file 1 – Preferential structural transitions between.docVIP

Supplementary data IV – Preferential structural transitions between LSPs We defined ten LSP groups characterizing preferential transitions of local structures in global protein structures. The groups were obtained in two steps: i) LSPs with transition probabilities larger than a threshold p=0.2 were first grouped then, ii) if the number of LSPs in the groups resulting in (i) was larger than 20, the threshold p was increased by step of 0.02 (until 0.4), until the number of LSPs in groups was smaller than 20. This procedure yielded to seven sub-networks of increasing preferential transitions (group n°1 composed of 5 LSPs; n°2, 12; n°3 and 4, 6; n°5, 16; n°6, 14; n°7, 9). Moreover, small sub-networks composed of less than 5 LSPs remained. In order to characterize them, these outliers were then clustered (R software 1) into three groups according to their size, i.e. the number of LSPs per sub-network, their maximum inner transition probability and the number of their outward transition probabilities more than 0.2. Three well separated groups emerged with 19, 22 and, 11 LSPs respectively. These groups are not sub-networks, their purpose is to gather very small sub-networks, even isolated LSPs, with similar transitional properties. They were named groups n°8, 9 and 10. These ten groups are described here. Only transitions larger than 0.2 (42.53 % of observed transitions) are represented and taken into account for statistics. Transitions with a probability comprised between 0.2 and 0.3 are shown with blue arrows. Green and yellow arrows show respectively 0.3 to 0.5 and 0.5 to 0.7 probability transitions. Red arrows show probability transitions more than 0.7. Circular nodes with respectively black and green border correspond to Helical and Connecting LSPs. Rectangular nodes with respectively red and blue border correspond to Extended and Extended edge LSPs. Category 1 Sub-network 1 is composed of 5 successive and per se overlapping LSPs, i.e. the Helical LSP 44 and four C