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 (BAPPL-Z)
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.
34. PROSECSC
PROTEIN SECONDARY STRUCTURE PREDICTION.
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.
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 (BAPPL-Z)
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.
34. PROSECSC
PROTEIN SECONDARY STRUCTURE PREDICTION.
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.
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