- All-in-1 bioinformatics tools: ExPASy
- Systems biology: Flux Balance Analysis
- Cancer database/webserver: TumorPortal, GDC, cBioPortal, GTExPortal, ICGC, TCGA, COSMIC, CancerResource,Oncomine, TIMER, GEPIA, DepMap
- Single Cell Expression database/webserver: EBIsc, Broad Institute, CancerSEA, scRNASeqDB, COMET
- DNA/Plasmid analysis: ApE
- Protein sequence alignment and analysis: ClustalX, STRAP, MEGA, WebLogo, BlockLogo, pLogo, PhyloBot
- Protein 3D structure modeling: Rosetta, ROSIE
- Protein crystallography: Phenix, CCP4, COOT, CNS
- Protein structure display: Pymol, VMD, Chimera, BioBlender
- Protein animations: Molecular Flipbook
- Mass spectrum: mMass, TopPIC, SPECTRUM
- Reference Manager: Papers, EndNote
- Molecular dynamics: NAMD, Gromacs, Amber, MDWeb
- Small-molecule docking: DOCK, AutoDock, AutoT&T
- Small-molecule database: Specs, ZINC, DrugBank, TCM, Asinex, Selleckchem, Prestwick, Ambinter, Enamine
- Molecule File Format conversion: I_Interpreter, MLOCSR
- Ligand-Protein analysis: LigPlot, PLIP
- Chem & bio informatics: Schrodinger
- Quantum chemistry computation and analysis: GAMESS, Gaussian, Multiwfn, IQmol, Avogadro
- Scientific plotting & picture processing: Prism, Inkscape, EazyDraw, R, Matlab, Graphviz, ImageJ, GNUplot
- Add H2O molecules to the interior space of proteins: DOWSER
- Predict the non-linear distance between two residues over the protein surface: Xwalk
- Linux tutorials:
- 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
- C++:
- Perl:
- Pymol tips & tricks
- http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol
- http://people.mbi.ucla.edu/sawaya/tutorials/Graphics/pymol.html
Hubei Bioinformatics Society