Protein Structure Prediction Software and Tools   [Help Hotline]


1. Bhageerath

An automated energy based protein tertiary structure prediction web server. Starting with sequence and secondary structure information, the web server predicts 5 native-like candidate structures for the protein.

2. Bhageerath H

A Homology ab-initio Hybrid Web server for Protein Tertiary Structure Prediction. Starting with sequence, the web server predicts 5 native-like candidate structures for the protein.

3. Protein Structure Generation

A utility to build a three dimensional structure based on the knowledge of protein sequence and secondary structure information.


4. Persistence Length

A biophysical filter, which calculates the maximum length of the polypeptide chain in one direction. It is one of the filters employed in the Bhageerath web server for rejection of the non-native like structures from the initial ensemble of trial structures


5. Radius of Gyration

A biophysical filter, which is related to the diameter of the protein structure. It is also currently a part of the Bhageerath web server and is utilized for rejection of non-native like structures.


6. Hydrophobicity

It comes under the category of biophysical filters, whereby it can help in accepting or rejecting a candidate structure depending on the ratio of accessible surface areas of the hydrophobic and hydrophilic residues.


7. Packing Fraction

It comes under the category of biophysical filters, whereby it can help to evaluate the value of packing fraction for a given protein and to find out whether the value is in acceptable limits for globular protein or not.



  Protein Regularity Index


9. Protein structure optimizer

Energy minimizer for proteins


10. ProSEE

Scoring Function for Protein Structure Evaluation Calculates intramolecular energy of a protein in component-wise break up.


11. Superimpose

Fits two molecules and calculates the RMSD between them.


12. Protein Angle Descriptor

Calculates the angles & dihedral in the main chain of the protein


13. BGPred(Beta Gamma Turn Predictor)

BG Pred web server predicts beta and gamma turns.





15. pcSM Software

pcSM: Capturing Native Protein Structures with a Physico-Chemical Metric.


15. Bhageerath-H Strgen

Bhageerath-H Strgen: A Web tool for protein decoy generation.


16. D2N

D2N: Distance to Native.


17. RM2TS

From Ramchandran Maps to Tertiary Structures of Proteins.


18. ProtSAV

A Protein Tertiary Structure Analysis and Validation Server.

19. SDIndex

A measure for reliable modelability of protein tertiary structure.

20. PvaxDB

A comprehensive structural repository of P. vivax soluble proteome.

21. Seq2Func

Protein Sequence to Function Prediction tool: A newer way of classifying amino acids based on chemical measures.

22. Seq2Enz

Protein Sequence to Enzyme Prediction tool: An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction.

23. S2F

A metaserver for protein sequence to function prediction: Integrates some popular protein annotation tools and furnishes the user with a set of consensus functional terms at a single platform with high reliability.

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