Disclaimer : All the information given in this page is based on the public websites and please let me know if there is any correction or need to be removed. email.
Cheminformatics Expert's Page Click here                                                                                  For Training and Queries Click here
​Resource Links Click here                                                                                                              Scientific Android Apps Click here

Online Powerful Chemical Editor

Molecular Visualization Tools

1. RasMol             -    Download
2. RasTop             -    Download
3. Swiss PDB         -    Download
4. Mercury            -    Download
5. Accelrys Viz      -    Download (Register)
6. PyMol               -    Download (Register)

Useful Tools

1. PDF Creator             -    Download
2. Image Creator         -    Download
3. Tutorial Creator       -    Download
4. CompressExtract     -    Download

Chemistry Tools

1. R goup Analysis           -   Download
2. Fragment Profile         -   Download
3. Molecular Framework   -   Download
4. Multiple Clustering       -   Download
5. Scaffold Activity          -   Download
6. Structure Standardizer -   Download
7. Tautomer Generator   -   Download
8. Structure Management-   Download

Chemical Databases

1. ChEMBL Bioactive Drug DB         -    Web Link
2. PUBChem - Bioassays ds DB        -    Web Link
3. A'E"bility of a Drug DB                -    Web link
4. ZINC Databases - Docking DB      -    Web Link
5. eMolecules DB                            -    Web Link
6. PubChem - BioActivity Service    -    Web Link

QSAR/ QSPR

1. e-DRAGON              -    Web Link
2. A-LogPS                 -    Web Link
3. 3D - QSAR              -    Web Link
4. Predict Property      -    Web Link
5. Mol-Info                 -    Web Link
6. QSAR Models           -    Web Link
7. Open 3D-QSAR        -    Download
8. 700-2/3D Descriptors    Download
9. Open MolGrid         -    Web Link
10. QSAR Equations     -    Web Link
11. DMax QSAR Tool    -    Download
12. cQSAR                  -    Web Link

Cheminformatics Tools

1. e-BABEL                        -    Web Link
2. OSRA (Image>Structure   -    Download
3. SMILES > Image              -    Web Link
4. MOLecular fingerPRINT    -    Web Link
5. NPC Datasets                 -    Download
6. Structure Conformer/2-3D    Web Link
7. Instant JChem               -    Download (Register)
8. Marvin Sketch, Beans     -    Download (Register)
9. JChem for Excel            -    Download (Register)
 

Quantum Chemistry

1. Huckel Molecular Orbital Package    -    Web Link
2. Web Based Interface    -    Web Link
Kohn-Sham wave-function    -    Web Link

Protein Modelling Tools

1. Modeller 9v8        -    Download
2. VegaZZ  2.4         -    Download
3. CPH Models         -    Web Link
4. PHYRE                -    Web Link
5. Scratch Pro         -    Web Link
6. I-Tasser              -    Web Link
7. ModBase             -    Web Link
8. SwissModel         -    Web Link

Molecular Dynamics Tools

1. GROMACS         -    Download 
2. Online CHARMm-    Web Link (Register)
3. Create Topology-    Web Link
4. NAMD 2.7         -    Download (Register)   View Tutorial
5. VegaZZ  2.4      -    Download
6. TINKER            -    Download

                               

Molecular Docking - AutoDock 4

Autodock in Windows requires the following software:
Install the software as per the serial number and works only in 32bit Windows 2000, XP & Vista.

1. Cygwin 1.7.8     -    Download
2. AutoDock 4.2    -    Download
3. Python 2.5.2     -    Download
4. MGLTools 1.5.4 -    Download

Autodock IV Simple Tutorial - View

Autodock IV Tutorial - Made Easy

Picture
Girinath G. Pillai

Read Tutorial          Download Tutorial
Autodock Lock File (Protein)
File Size: 321 kb
File Type: pdb
Download File
Autodock Key File (Ligand)
File Size: 11 kb
File Type: pdb
Download File

Binding Site Prediction

1. CAVER                -    Web Link (Register)
2. 3D LigandSite      -    Web Link
3. PharmMapper      -   Web Link
4. PASS                  -    Web Link
5. Reverse 3D Screen-    Web Link
6. FindSite              -    Web Link

Molecular Docking Tools

1. Swiss DOCK           -    Web Link
2. PLATINUM             -    Web Link
3. Docking Server     -    Web Link (Register)
4. DOCK                   -    Web Link
5. Rosetta Commons -    Web Link
6. Argus Lab             -    Download (Register)
6. LeadIT                 -    Download(Register)      Tutorial

ADME/T

1. Virtual Tox lab       -    Web Link
2. STITCH - Network  -    Web Link
3. Predict Toxicity     -    Web Link
4. ADME Software      -    Web Link
5. Toxicity Prediction -    Web Link
6. Free ADME Tools    -    Web Link (Register)
7. Predict ADMET       -    Web Link

Ligand Design

1. Residue DEPTH        -    Web Link
2. GANDI - De - Novo   -    Web Link
3. Feature Trees         -    Web Link
4. Reverse 3D Screen   -    Web Link
5. e-LEA3D - De-Novo  -    Web Link

Biological Databases

1. Protein Databases
        i. UniProt        -    Web Link 
       ii. EBI ProDB     -    Web Link
      iii. NCBI ProDB   -    Web Link
      iv. ProClass-PIR  -    Web Link
       v. HumanProRef-    Web Link 

2. Nucleotide Databases
        i. DDBJ            -    Web Link 
       ii. EBI NucDB     -    Web Link
      iii. NCBI NucDB   -    Web Link

3. Structural Databases
        i. RCSB-PDB        -    Web Link 
       ii. EBI PDBe         -    Web Link
      iii. NCBI MMDB      -    Web Link
      iv. CATH              -    Web Link
       v. SCOP              -    Web Link 

Online Tools

1. Database Heuristic Searches
        i. NCBI-BLAST       -    Web Link 
       ii. EBI-FASTA         -    Web Link
      iii. Sanger-PFam     -    Web Link
      iv. ProSite             -    Web Link

2. Sequence Analysis
        i. Blast2Seq         -    Web Link 
       ii. ClustalW-EBI     -    Web Link
      iii. TCoffee-EBI      -    Web Link

3. Comparitive Tools

4. Tutorials
        i. Biological DB     -    View Tutorial
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