Table 5.

A list of modules of Bhageerath converted to independent web utilities with their respective URL's

Sl. No.	Name of the utility	Description
1	Persistence length filter (http://www.scfbio-iitd.res.in/software/proteomics/perlen.jsp)	A filter based on the maximum uninterrupted length of the polypeptide chain persisting in a particular direction
2	Radius of gyration filter (http://www.scfbio-iitd.res.in/software/proteomics/rg.jsp)	A filter based on the radius of the molecule and defined as the root mean square distance of the collection of atoms from their common centre of gravity
3	Hydrophobicity ratio filter (http://www.scfbio-iitd.res.in/software/proteomics/hyphb.jsp)	A filter based on hydrophobicity ratio, which is defined as the ratio of loss in accessible surface area (ASA) per atom of non-polar atoms to the loss in accessible surface area per atom of the polar atoms
4	Packing fraction filter (http://www.scfbio-iitd.res.in/software/proteomics/pf.jsp)	A filter based on packing density, which utilizes observation that proteins are known to exhibit packing fractions ∼0.7
5	Protein structure optimizer (http://scfbio-iitd.res.in/software/proteomics/promin.jsp)	A utility that minimizes the energy of the protein structure using a combination of steepest descent and conjugate gradient minimization algorithms
6	Scoring function for protein structure evaluation (http://www.scfbio-iitd.res.in/utility/proteomics/energy.jsp)	An all-atom empirical energy based scoring function which combines second generation force field parameters with a hydrophobicity function
7	Protein regularity index (http://www.scfbio-iitd.res.in/software/proregin.jsp)	A utility based on the regularity seen in the main chain loop dihedral angles of proteins