# Computational Structural Biology Lab

**Source**: http://www.csb.iitkgp.ac.in/applications/HotSPRing/docs/references.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)

1. Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W. et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. *Acta Crystallographica Section D*, **66**, 213-221.
2. Barik, A., C, N., Pilla, S.P. and Bahadur, R.P. (2015) Molecular architecture of protein-RNA recognition sites. *J. Biomol. Struct. Dyn.*, 1-14.
3. Bahadur, R.P., Zacharias, M. and Janin, J. (2008) Dissecting protein-RNA recognition sites. *Nucleic Acids Res.*, **36**, 2705-2716.
4. Breiman, L. (2001) Random Forests. Machine Learning, **45**, 5-32.
5. Hubbard SJ (1992). NACCESS: A program for calculating accessibilities. Department of Biochemistry and Molecular Biology. University College of London.
6. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. *Bioinformatics*, **23**, 2947-2948.
7. McDonald IK and Thornton JM (1994). Satisfying hydrogen bonding potential in proteins. *J. Mol. Biol*. **238**, 777-793.
8. Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R. and Dubourg, V. (2011) Scikit-learn: Machine learning in Python. *The Journal of Machine Learning Research*, **12**, 2825-2830.
9. Schneider, R. and Sander, C. (1996) The HSSP database of protein structure-sequence alignments. *Nucleic Acids Res.,* **24**, 201-205.
10. Shannon,C. (1948) A mathematical theory of communication. *Bell Syst. Tech. J.,* **27**, 379--423.