# 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

- [Home](http://www.csb.iitkgp.ac.in/)
- [Research](http://www.csb.iitkgp.ac.in/pages/research.php)
- [Publications](http://www.csb.iitkgp.ac.in/pages/publications.php)
- [Teaching](http://www.csb.iitkgp.ac.in/pages/teaching.php)
- Tutorials
  - [Python Tutorial](http://www.csb.iitkgp.ac.in/tutorials/python/python_index.php)
  - [Gromacs Tutorial](http://www.csb.iitkgp.ac.in/tutorials/gromacs/gromacs_index.php)
- Tools
  - [PRince](http://www.facweb.iitkgp.ac.in/~rbahadur/prince/home.html)
  - [Layers](http://www.csb.iitkgp.ac.in/applications/mol_layers/main.php)
  - [HotSPRing](http://www.csb.iitkgp.ac.in/applications/HotSPRing/main.php)
  - [NCodR](http://www.csb.iitkgp.ac.in/applications/NCodR/index.php)
  - [Nucpred](http://www.csb.iitkgp.ac.in/applications/Nucpred/index.php)
  - [pmiRScan](http://www.csb.iitkgp.ac.in/applications/pmiRScan/index.php)
  - [proRBR](http://www.csb.iitkgp.ac.in/applications/proRBR/index.php)
  - [Rotamers for RBPs](http://www.csb.iitkgp.ac.in/applications/RBP-Rotamer/rotamer.php)
  - [MetIoR](http://www.csb.iitkgp.ac.in/applications/MetIoR/index.php)
- Databases
  - [PMMLID](http://www.csb.iitkgp.ac.in/databases/miR_details/index.php)
  - [TFNRDv1.0](http://www.csb.iitkgp.ac.in/databases/TFNRDv1.0/tfnrd.html)
  - [ProRBR Dataset](http://www.csb.iitkgp.ac.in/applications/proRBR_dataset/proRBR.php)
- Benchmarks
  - [Protein-RNA Docking Benchmark version 3](http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php)
  - [Protein-RNA Docking Benchmark version 2](http://www.csb.iitkgp.ac.in/applications/PRDBv2.php)
  - [Protein-RNA Docking Benchmark version 1](http://www.csb.iitkgp.ac.in/applications/benchmark.php)
  - [Protein-RNA Affinity Benchmark](http://www.csb.iitkgp.ac.in/applications/PRDBv3/Affinity.php)
- [Members](http://www.csb.iitkgp.ac.in/pages/members.php)
- Links
  - [Bioinformatics Centre](http://www.csb.iitkgp.ac.in/bioinformatics_centre/index.html)
  - [Homepage IITKGP](http://www.iitkgp.ac.in)
  - [Homepage Department of Biotechnology](http://www.bt.iitkgp.ac.in)
- [Contact](http://www.csb.iitkgp.ac.in/pages/contact.php)

- [Tutorial](http://www.csb.iitkgp.ac.in/applications/HotSPRing/docs/tutorial.php)
- [Instructions](http://www.csb.iitkgp.ac.in/applications/HotSPRing/docs/instructions.php)
- [References](http://www.csb.iitkgp.ac.in/applications/HotSPRing/docs/references.php)
- [HotSPRing](http://www.csb.iitkgp.ac.in/applications/HotSPRing/main.php)

### 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](http://www.bioinf.manchester.ac.uk/naccess/).
- The program HBPLUS has been used for the hydrogen bonds calculations. It can be downloaded [here](http://www.ebi.ac.uk/thornton-srv/software/HBPLUS/).
- The program CLUSTALW was used for aligning the bound and unbound sequences. It can be downloaded [here](http://ftp.ebi.ac.uk/pub/software/clustalw2/).
- The program PHENIX has been used for the rmsd calculations. It can be downloaded [here](https://www.phenix-online.org/).
- 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.

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