Supercomputing Facility for Bioinformatics &
Computational Biology, IIT Delhi
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Bioinformatics Software and Tools
1. Gene Predictor(ChemGenome 2.0)
    Whole Genome Analysis
2. Bhageerath
    Predicts native-like structures for small globular proteins 
3. Sanjeevini
    A complete drug design software. 
4. Binding Affinity Prediction of Protein-Ligand Server(BAPPL)
    Computes the binding free energy of a protein-ligand complex.
5. Binding Affinity Prediction of Protein-Ligand complex containing Zinc Server
    Computes the binding free energy of a metalloprotein-ligand complex containing     zinc.
6. Drug-DNA Interaction Energy (PreDDICTA)
    Calculates the Drug-DNA interaction energy.
7. ParDOCK - Automated Server for Rigid Docking
    Predicts the binding mode of the ligand in receptor target site.
8. Active Site Prediction

9. Automated Version Of Active Site Prediction (AADS)

   Predicts 10 binding sites in a protein target and docks the uploaded ligand molecule    at all 10 sites predicted in an automated mode.
10. DnaDOCK - Dna Ligand Docking
    All-atom energy based Monte Carlo DNA ligand docking
11. Non Redundant Database of Small Molecules
      Virtual high throughput screening of small molecules and their optimization into       lead like candidates.
12. Lipinski Filters
     Checks whether a drug satisfies the 5 Lipinski rules.
13. DNA Sequence to Structure
     Generates double helical secondary structure of DNA using conformational      parameters taken from experimental fiber-diffraction studies.
14. Hydrogen Addition to Nucleic Acid
      Adds the hydrogen coordinates to the X-ray crystal structures of Nucleic acids
15. Hydrogen Addition to Protein
       Adds the hydrogen coordinates to the X-ray crystal structures of Proteins.

16. Gene Evaluator(ChemGenome 1.1)
    Characterizes a DNA sequence as gene or nongene

17. Protein Structure Generation

    Structure Generation from given dihedrals
18. Persistence Length
    Filters for Globular Protein Evaluation
19. Radius of Gyration
    Filters for Globular Protein Evaluation

20. Hydrophobicity

    Filters for Globular Protein Evaluation

21. Packing Fraction

    Filters for Globular Protein Evaluation
22. ProRegIn
    Protein Regularity Index
23. Protein structure optimizer
    Energy minimizer for proteins
24. ProSEE
    Scoring Function for Protein Structure Evaluation Calculates intramolecular energy     of a protein in component-wise break up.
25. Superimpose
    Fits two molecules and calculates the RMSD between them.
26. Protein Angle Descriptor
    Calculates the angles & dihedral in the main chain of the protein

27. Wiener Index Calculator

    This tool is useful for calculating Wiener index.

28. RASPD for Preliminary Screening of Drugs

    This tool is useful for preliminary screening of drug molecules based on Wiener       index calculation. This will predict binding energy of drug/target at a preliminary      stage.
29. BGPred(Beta Gamma Turn Predictor)
    BG Pred web server predicts beta and gamma turns.
30. Volume Calculator
     Calculates the volume of a molecule

31. Melting Temperature Predictor (For oligonuclotide)

    It predicts the melting temperature of short DNA sequences (upto 70 base pairs)     at a user defined salt within the specified range.

32. Genome analysis by melting

It predicts the melting temperature for longer(>70 bases) DNA sequences, and it also gives the melting profile for the sequence.

33. Transferrable Partial Atomic Charge Model - up to 4 bonds (TPACM4)

    This tool is used for assignment of partial atomic charge of small molecules.



35. Gene Predictor(ChemGenome 3.0)

   ChemGenome 3.0 is a gene prediction tool that takes a whole genome sequence or    a part of the genome of a prokaryote or virus as input and predicts genes along    with their coressponding protein sequences in all the six reading frames.

36.Bhageerath H

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

37. pcSM Software
    pcSM: Capturing Native Protein Structures with a Physico-Chemical Metric.
38. MD Parameter based Tm Predictor