Resource

This page contains useful resources for both Computational biology/Bioinformatics and Experimental Biology research conducted in our lab. Enjoy!

  1. All-in-1 bioinformatics tools: ExPASy
  2. Systems biology: Flux Balance Analysis
  3. Cancer database/webserver:     TumorPortal, GDCcBioPortalGTExPortalICGCTCGACOSMIC, CancerResource,Oncomine, TIMER, GEPIA, DepMap 
  4. Single Cell Expression database/webserver: EBIsc, Broad Institute, CancerSEA, scRNASeqDB, COMET
  5. DNA/Plasmid analysis: ApE
  6. Protein sequence alignment and analysis: ClustalX, STRAP, MEGA, WebLogo, BlockLogo, pLogo, PhyloBot
  7. Protein 3D structure modeling: Rosetta, ROSIE
  8. Protein crystallography: Phenix, CCP4, COOT, CNS  
  9. Protein structure display: PymolVMD, Chimera, BioBlender
  10. Protein animations: Molecular Flipbook
  11. Reference Manager: Papers, EndNote
  12. Molecular dynamics: NAMD, Gromacs, Amber, MDWeb
  13. Small-molecule docking: DOCK, AutoDock, AutoT&T
  14. Small-molecule database: Specs, ZINC, DrugBank, TCM, Asinex, Selleckchem, Prestwick, Ambinter, Enamine
  15. Molecule File Format conversion: I_Interpreter
  16. Ligand-Protein analysis: LigPlot, PLIP
  17. Chem & bio informatics: Schrodinger
  18. Scientific plotting & picture processing: Prism, Inkscape, EazyDraw, R, Matlab, GraphvizImageJ, Grace (Xmgrace)
  19. Add H2O molecules to the interior space of proteins: DOWSER
  20. Predict the non-linear distance between two residues over the protein surface: Xwalk
  21. Linux tutorials:
  22. Python tutorials:
  23. C++:
  24. Perl:
  25. 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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