Control Panel of CytoKavosh, including the CytoKavosh control tab for getting input parameters.

<p>The right side of the figure shows the ‘results’ table panel after running the CytoKavosh for given input parameters. A table for each run of plug-in appears in the separate tab in ‘result’ panel. These tabs keep the results until finishing the plug-in. For larger sizes of the motifs, the number of detected motifs increases exponentially. So, the ‘results’ table can be explored page by page. The below panel shows the graphical representation of selected motif in the table.</p

The implicit built trees rooted at vertex 1 of size 4 for network in <b>Figure 1</b>.

<p>(a) Trees built according to (1,1,1) pattern. According to this pattern, after selecting vertex 1 in root, one of its neighbors must be selected, so the second selected vertex is vertex 2. Continuing the selecting process, one of the neighbors of the vertex 2 (vertex 6) and after that vertex 4 is selected. All chosen vertices are shown by specified circles in these figures. (b) Trees built according to (1,2) pattern. (c) Trees built according to (2,1) pattern. (d) Tree built according to (3) pattern.</p

Execution results of some sample networks, related to 4 to 7 motif sizes with 100 random network sizes.

<p>Rows indicate the running time (seconds) of the studied tool for each motif size.</p

A sample of exported motif in a new network view.

<p>A sample of exported motif in a new network view.</p

Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers

Antimicrobial peptides (AMPs) are part of the innate host defense system, and they are produced by living organisms to defend themselves against infections. Pardaxin is a cationic AMP with antimicrobial and antitumor activities that has potential to be used as a novel antibiotic or for drug delivery in cancer therapy. This peptide acts on the membrane of target cells and can lead to lysis using different mechanisms of action. Here, we conducted 4.5 <i>μs</i> all-atom molecular dynamics (MD) simulations to determine the critical fragments and residues of Pardaxin for early insertion into different lipid bilayers. Our results revealed that the N-terminal domain of the peptide, particularly the Phe 2 and (/or) Phe 3 residues, has a crucial role in early insertion, independent of the type of lipid bilayers