Factor scores for the first four principal components.

<p>The different colored lines are the natural separation of the results into the different simulation runs.</p

The original (template) network that gave rise to the data and the two best networks obtained from minimizing the error.

<p>The network connectivities as well as the reaction probabilities were optimized in order to obtain the minimal deviation between the model and “data” values.</p

The optimal (template) network and the best network inferred from minimizing the RMSD between the two expression levels.

<p>Only the network connectivities were optimized. All other parameters including the kinetic parameters were kept constant. Although the two networks are very similar, there is a slight difference in the activation of P1 and P2.</p

Factor Loadings–Correlation coefficients between original variables and components

<p>Factor Loadings–Correlation coefficients between original variables and components</p

The abstract representation in our model of the network shown in Figure 1(a) is shown in Figure 1(b).

<p>The gene corresponding to each protein is represented by different colors. Each protein (colored gray) has a certain number of binding domains. For eg., protein P1 can bind to genes G1, G3 and G4 (showed by the colored bars). The red and green boxes refer to the effect of binding while the red and green circles refer to PTMs.: red represents repression and green, activation</p

Correlation coefficient of the individual runs for the three different networks against one another.

<p>The correlation coefficients are computed as the correlation of the three protein levels for each run and plotted as a matrix with the different runs making up the abscissa and ordinate. Runs 1–25 pertain to the template network, 26–50 to the first optimized network (R2) and runs 51–75 to the second optimized network (R3). The colors range from blue (very low correlation) to dark brown (high correlation). The fact that there is no clear discrimination between the networks implies that the protein levels obtained from the three networks occupy similar regions in phase-space.</p

The GANDivAWeb User Interface: The figure shows the user interface for gandivaweb with snapshots of the different tabs corresponding to the main functionalities shown

<p><b>Copyright information:</b></p><p>Taken from "GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures"</p><p>http://www.biomedcentral.com/1472-6807/8/15</p><p>BMC Structural Biology 2008;8():15-15.</p><p>Published online 7 Mar 2008</p><p>PMCID:PMC2275735.</p><p></p

Species present in our model

<p>Species present in our model</p

“Equilibrium” phase space for proteins 1, 3 and 4.

<p>The reaching of equilibrium was assessed by the stabilization of the protein levels on almost invariant values. In our case, the protein levels at a time corresponding to 300 seconds were assumed to indicate equilibrium levels. There is a lack of a clear separation of the protein levels from the three different networks.</p

The reactions taking place in our system

<p>The reactions taking place in our system</p