Table 5.
Some Important Nano-Informatics-Related Databases, Software, and Tools.
| Sl. No. | Name | Details | URL Link |
|---|---|---|---|
| Databases | |||
| 1. | Nanomaterial Biological Interactions Knowledgebase | This database serves as a depository for annotated data on nanomaterial characterization (purity, size, shape, charge, etc), synthesis methods, and nanomaterial-biological interactions. | http://nbi.oregonstate.edu |
| 2. | ISA-TAB-Nano | The ISA-TAB-Nano standard is specific for the format, of how nanomaterials, small molecules, and biological specimens can be represented and shared data using the spreadsheet or TAB-delimited files. | http://ceint.duke.edu/research/nikc/isa-tab-nano |
| 3. | Nano-HUB database | Nano-HUB provides a searching platform for an online database of nano bio tools. | https://nanohub.org/resources/databases |
| 4. | Toxicology Data Network | Includes and connects databases on toxicology, hazardous chemicals, environmental health, and toxic releases | TOXNET: Toxicology Data Network Fact Sheet (archive-it.org) |
| 5. | OECD | Deals with the safety issues of manufactured nanomaterials. | - |
| Modeling & visualization tools | |||
| 6. | Avogadro | Molecular editor and visualizer. | Avogadro - Free cross-platform molecular editor - Avogadro |
| 7. | PyMOL | PyMOL is an open-source but proprietary molecular visualization system. Downloadable. | https://pymol.org/ |
| 8. | UCSF Chimera | The integrated visualization and analysis of molecular structures and related nonstructural biological data are made possible by web-based computing resources. | www.cgl.ucsf.edu > chimera |
| 9. | VMD | The molecular visualization program displays animate and analyzes large biomolecular systems using 3-D graphics and built-in scripting. | www.ks.uiuc.edu/Research/vmd |
| 10. | ChemSketch | A molecular modeling program creates and modifies images of chemical structures. | www.acdlabs.com/resources/ freeware/ chemsketch |
| Docking & interactions | |||
| 11. | Autodock 4 | Automated docking tools are designed and developed for docking studies and analysis. Small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure and are predicted. | https://autodock.scripps.edu |
| 12. | PatchDock | Molecular Docking Algorithm Based on Shape Complementary Principles and provide results with scoring values of each complex. | https://bioinfo3d.cs.tau.ac.il/PatchDock/php.php |
| 13. | Hex | Hex is an interactive protein docking and molecular superposition program. | hex.loria.fr/licence-8.0.0.html |