Step 2: Select a chain identifier from the list

Step 3: Choose the node type for the generation of protein contact network either considering all the atoms or the alpha carbon of each amino acid as a node

Step 4: Select the cut-off distance for determining the neighboring contacts for each amino acid (cut-off distance range from 5 to 12 Angstrom) and click the “submit” button

Step 5: K-core result page contains i) MDL plugin, ii) result table and iii) amino acid details for each core

i) MDL plugin – This plugin works only upon installation of the Chime plugin or the user can download the pdb file for each core to visualize it using any molecular visualization software. The “display” option is provided for each core to display the protein structure using MDL plugin.

ii) Result table – This table provides four columns such as number of k-cores, total number of amino acids in each core, pdb file for each core and display option for each core.

iii) Amino acid details for each core – “Results” link will display the amino acid numbers for each core

 
Step 6: To view the protein structure for each core you must install the MDL chime plug-in software.