Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

The webserver may take a few seconds to calculate the parameters and generate the output

• The webserver may take a few seconds to calculate the parameters and generate the output.
• Users are advised not to press the refresh/back button while calculations are going on.
• The users are advised to upload only the PDB format (.pdb) and HSSP format files (.hssp) with same name.
• If the webserver displays some error, please try again. Also ensure the correctness of file formats uploaded. Contact the authors if the problem persists.
• The program NACCESS has been used to calculate the solvent accessible surface area. It can be downloaded here.
• The program HBPLUS has been used for the hydrogen bonds calculations. It can be downloaded here.
• The program CLUSTALW was used for aligning the bound and unbound sequences. It can be downloaded here.
• The program PHENIX has been used for the rmsd calculations. It can be downloaded here.
• Random Forest based model is used for prediction of range of ΔΔG values.
• The test run button gives an output for a test run using the file 1DFU.pdb.

Important instructions before using the server

• To enter multiple chain ids, enter them directly without any space or separator e.g. MN.
• The webserver can handle up to eight protein chains and eight RNA chains with a maximum limit of 20,000 amino acids and 20,000 nucleotides respectively.
• The files generated will be available for download until 30 minutes after program execution.
• The probe size used for running NACCESS is 1.40 Å.