Table 3.

List of Tools Available for Protein Tertiary Structure Prediction

Sl. No	Softwares	URLs	Description
1.	CPHModels3.0	http://www.cbs.dtu.dk/services/CPHmodels/	Protein homology modeling server
2.	SWISS-MODEL	http://swissmodel.expasy.org/SWISS-MODEL.html	A fully automated protein structure homology-modeling server
3.	Modeller	http://salilab.org/modeller/	Program for protein structure modeling by satisfaction of spatial restraints
5.	3D-JIGSAW	http://3djigsaw.com/	Server to build three-dimensional models for proteins based on homologues of known structure
6.	PSIPRED	http://bioinf.cs.ucl.ac.uk/psipred/	A combination of methods such as sequence alignment with structure based scoring functions and neural network based jury system to calculate final score for the alignment
7.	3D-PSSM	http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html	Threading approach using 1D and 3D profiles coupled with secondary structure and solvation potential
8.	ROBETTA	http://robetta.bakerlab.org	De novo Automated structure prediction analysis tool used to infer protein structural information from protein sequence data
9.	PROTINFO	http://protinfo.compbio.washington.edu/	De novo protein structure prediction web server utilizing simulated annealing for generation and different scoring functions for selection of final five conformers
10.	SCRATCH	http://scratch.proteomics.ics.uci.edu/	Protein structure and structural features prediction server which utilizes recursive neural networks, evolutionary information, fragment libraries and energy
11.	I-TASSER	http://zhanglab.ccmb.med.umich.edu/I-TASSER/	Predicts protein 3D structures based on threading approach
12.	BHAGEERATH	http://www.scfbio-iitd.res.in/bhageerath/index.jsp	Energy based methodology for narrowing down the search space of small globular proteins
13.	BHAGEERATH-H	http://www.scfbio-iitd.res.in/bhageerath/bhageerath_h.jsp	A Homology ab-initio Hybrid Web server for Protein Tertiary Structure Prediction