We have provided a
.pqr file 1o3b.pqr for download in the example panel on the home page page of BION-2 webserver. We encourage users to download it and use it for an example run. Once user has downloaded the provided
.pqr file (
1ob3.pqr) on their computer locally. She/he can use it as input
.pqr format structure file as shown below.
Then she/he should be able to choose the ion-type (presentaly we choose Ca2+), number of predictions (currently we choose default 5), Internal dielectric for the Gaussian dielectric model (we choose default 2) and ionic strength (default value 0.15M). After choosing all the required parameters values they can click on the submit button to make the predictions. After clicking submit it proceeds to make prediction if the inputs are valid, otherwise if there are issues with the input it is reported. The whole process takes areound 1 to 2 minutes, and user is redirected to the results page, which lists the postions of predicted ion positions and potentials, in addition a visualization of the protein with predicted ions is also provided for visual aid. The typical output for the present case looks as shown below.