Strider acts on coordinate files in PDB format. So, for estimating potential steric hindrance sites in a single molecule or molecule complex, user has to upload the coordinates in PDB file format and has to choose any one of the two given options “inter” or “intra”. Here, “inter” option finds the short contacts between atoms from different chains and “intra” option finds the short contacts between atoms from same chain.

    Output of every PDB file processed through STRIDER is assigned a unique JOB ID that is shown in result page. This molecule id can be used by the user to retrieve the output of a submitted job, after closing the session. Job ID is essential when user is submitting a larger molecule. As the processing of molecule and estimation takes some time. So, user can close the browser after submitting the file and noting the job ID. Later, user can use this job ID to retrieve the output of a submitted job. This molecule ID expires in 7 days. This means, a user can access STRIDER processed output within a week only.

    STRIDER server has embeded JSmol applet to view 3 dimensional structures of the submitted molecule. This is an interactive window for the user. User can rotate, zoom in, zoom out and change different representation of the molecule for better visualization.
    The sites of steric hindrance region are shown by yellow dotted lines connecting the two atoms.