About the server:
The MCTBI model predicts metal ions effects for RNAs and DNAs, including ion binding sites, ion-mediated electrostatic free energy, binding fraction of ions.
About the input parameters
(1) Temperature The unit is Celsius.
(2) Ion condition
  • (a) Monovalent ions: [Na+] or [K+].
  • (b) Divalent ions: [Mg2+].
  • (3) RNA structure The file must be in the PDB format. We set a 256-nucleotide sequence length limit in order to save the computational time. Atom types not in natural RNA (or DNA) will be eliminated in the calculation.
    (4) Job name User may define a job name. Only alphanumeric characters are allowed. The job name is required for checking job status.
    (5) Email address Email address is optional. If the email address is provided, the job results will be sent via email, otherwise, the results can be downloaded from the server according to the Job name and job ID .
    After the above input parameters are provided, the users may click "Calculate" button to submit the job.
    After the job is submitted:
  • The user will see two tables, one for the input parameters such as the temperature and ionic conditions, one for the job name, job ID, and status of the job: Processing, Pending, Running, or Done. It is important to save the job name and ID in order to check job status.