Resources

This page contains useful resources for both Computational and Experimental research conducted in our lab. Enjoy!
  1. All-in-1 bioinformatics tools: ExPASy
  2. Systems biology: Flux Balance Analysis
  3. DNA/Plasmid analysis: ApE
  4. Protein sequence alignment and analysis: ClustalX, STRAP, MEGA, WebLogo, BlockLogo, pLogo, PhyloBot
  5. Protein 3D structure modeling: Rosetta, ROSIE
  6. Protein structure display: PymolVMD, Chimera, BioBlender
  7. Protein animations: Molecular Flipbook
  8. Reference Manager: Papers, EndNote
  9. Molecular dynamics: NAMD, Gromacs, Amber
  10. Small-molecule docking: DOCK, AutoDock
  11. Small-molecule database: Specs, ZINC, DrugBank, TCM, Asinex, Selleckchem, Prestwick, Ambinter, Enamine
  12. Ligand-Protein 2D plot: LigPlot
  13. Chem & bio informatics: Schrodinger
  14. Scientific plotting & picture processing: Prism, Inkscape, EazyDraw, R, Matlab, GraphvizImageJ, Grace (Xmgrace)
  15. Add H2O molecules to the interior space of proteins: DOWSER
  16. Predict the non-linear distance between two residues over the protein surface: Xwalk
  17. Linux tutorials:
  18. Python tutorials:
  19. C++:
  20. Perl:
  21. Pymol tips & tricks
    • http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol
    • http://people.mbi.ucla.edu/sawaya/tutorials/Graphics/pymol.html

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