Computational Structural Biology Lab
Source: http://www.csb.iitkgp.ac.in/applications/HotSPRing/docs/instructions.php Parent: http://www.csb.iitkgp.ac.in/applications/HotSPRing/main.php
Department of Bioscience and Biotechnology Indian Institute of Technology Kharagpur
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- HotSPRing
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.