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, GDC, cBioPortal, GTExPortal, ICGC, TCGA, COSMIC, 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: Pymol, VMD, Chimera, BioBlender
10. Protein animations: Molecular Flipbook
11. Mass spectrum: mMass, TopPIC, SPECTRUM
12. Reference Manager: Papers, EndNote
13. Molecular dynamics: NAMD, Gromacs, Amber, MDWeb
14. Small-molecule docking: DOCK, AutoDock, AutoT&T
15. Small-molecule database: Specs, ZINC, DrugBank, TCM, Asinex, Selleckchem, Prestwick, Ambinter, Enamine
16. Molecule File Format conversion: I_Interpreter, MLOCSR 
17. Ligand-Protein analysis: LigPlot, PLIP
18. Chem & bio informatics: Schrodinger
19. Quantum chemistry computation and analysis: GAMESS, Gaussian, Multiwfn, IQmol, Avogadro
20. Scientific plotting & picture processing: Prism, Inkscape, EazyDraw, R, Matlab, Graphviz, ImageJ, GNUplot
21. Add H₂O molecules to the interior space of proteins: DOWSER
22. Predict the non-linear distance between two residues over the protein surface: Xwalk
23. Linux tutorials:
    • Tutorial Introduction to UNIX Commands
    • University of Surrey Unix Terminal Tutorials
    • Linux Command: Learning the Shell
    • SGE Queueing System
24. Python tutorials:
    • in-depth tutorial: http://docs.python.org/3.3/tutorial/
    • interactive tutorial: http://www.learnpython.org/
    • http://www.cogsci.rpi.edu/~destem/gamedev/python.pdf
    • http://pythonkit.com/Python-Cheat-Sheet-download-w370.pdf
25. C++:
    • Teach yourself C++ in 21 days
26. Perl:
    • Teach yourself Perl in 21 days
    • Perl in 24 hours
27. Pymol tips & tricks
    • http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol
    • http://people.mbi.ucla.edu/sawaya/tutorials/Graphics/pymol.html