Link

• Cryo-electron microscopy (cryo-EM)
• Nuclear magnetic resonance spectroscopy (NMR)
• X-ray crystallography
• Small angle X-ray scattering (SAXS)
• Molecular dynamics (MD)
• Bioinformatics

Here, we introduce useful tools such as software and database, which are commonly used in our research fields. We would like to encourage ourselves to collect information smoothly or collaborate between different research fields by sharing the knowledge through this page.

Cryo-electron microscopy (cryo-EM)

• Software

  • Xmipp(http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/WebHome)
  • EMAN(http://blake.bcm.edu/emanwiki/EMAN2)
  • RELION(https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page)

• Database

  • EMDataBank(http://www.emdatabank.org/)
  • EM Navigator(https://pdbj.org/emnavi/)

Nuclear magnetic resonance spectroscopy (NMR)

• Data processing

  • NMRPipe(https://www.ibbr.umd.edu/nmrpipe/index.html)
  • Azara(http://www2.ccpl.un.ac.uk/azara/)

• Spectral Analysis

  • Sparky(https://www.cgcsf.edu/home/sparky/)
  • CcpNmr analysis(https://www.ccpn.ac.uk/v2-software/software/analysis)
  • CARA(http://cara.nmr.ch/doku.php)
  • NMRView

• Structure calculation

  • CYANA(http://www.cyana.org/wiki/index.php/Main_Page)
  • XPLOR-NIH(https://nmr.cit.nih.gov/xplor-nih/)
  • TALOS+(https://spin.niddk.nih.gov/bax/software/TALOS/)
  • CS-ROSETTA(https://spin.niddk.nih.gov/bax/software/CSROSETTA/)
  • HADDOCK(http://www.bonvinlab.org/software/haddock2.2/)

• Structure evaluation

  • MolProbity(http://molprobity.biochem.duke.edu)

• Chemical shift prediction from structure

  • SPARTA+(https://spin.niddk.nih.gov/bax/nmrserver/sparta/)
  • SHIFTX2(http://www.shiftx2.ca/performance.html)

• Automated signal assignment

  • ARIA(http://aria.pasteur.fr)
  • MARS(http://www3.mpibpc.mpg.de/groups/zweckstetter/_links/software_mars.htm)

• Relaxation Analysis

  • relax(http://www.nmr-relax.com)
  • Modelfree4(http://www.palmer.hs.columbia.edu/software/modelfree.html)

• Database

  • BMRB(http://www.bmrb.wisc.edu/)

X-ray crystallography

• Synchrotron radiation facilities

  • ESRF(http://www.esrf.eu/)
  • ALS(https://als.lbl.gov/)
  • SPring-8(http://www.spring8.or.jp/)
  • LCLS(https://lcls.slac.stanford.edu/)
  • SACLA(http://xfel.riken.jp/index.html)

• Software

  • CCP4(http://www.ccp4.ac.uk/)
  • Phenix(https://www.phenix-online.org/)
  • CrystFEL(http://www.desy.de/~twhite/crystfel/)

• Model building

  • Coot(https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/)

• Structure evaluation

  • MolProbity(http://molprobity.biochem.duke.edu)
  • DSSP(http://swift.cmbi.ru.nl/gv/dssp/)
  • MINT(http://mint.cent.uw.edu.pl/)

• Database

  • Protein database (PDB)(https://www.wwpdb.org/)
  • Nucleic acid database (NDB)(http://ndbserver.rutgers.edu/)
  • Promode Elastic(https://pdbj.org/promode-elastic)

Small angle X-ray scattering (SAXS)

• Review article:http://scripts.iucr.org/cgi-bin/paper?S1600576717007786

• Software

  • CRYSOL(https://www.embl-hamburg.de/biosaxs/crysol.html)
  • GNOM(https://www.embl-hamburg.de/biosaxs/gnom.html)
  • DAMMIN(https://www.embl-hamburg.de/biosaxs/dammin.html)
  • GASBOR(https://www.embl-hamburg.de/biosaxs/gasbor.html)

Molecular dynamics (MD)

• MD software

  • GENESIS(http://www.aics.riken.jp/labs/cbrt/)
  • CHARMM(https://www.charmm.org/charmm/)
  • AMBER(http://ambermd.org)
  • GROMACS(http://www.gromacs.org)
  • NAMD(http://www.ks.uiuc.edu/Research/namd/)
  • TINKER(https://tinkertools.org/)
  • DESMOND
  • GROMOS(http://www.gromos.net/)

• Force Field

  • CHARMM(http://mackerell.umaryland.edu/charmm_ff.shtml)
  • AMBER(http://ambermd.org/AmberModels.php)
  • OPLS(http://zarbi.chem.yale.edu/oplsaam.html)
  • GROMOS(http://www.gromos.net/)
  • Slipids(ttp://www.fos.su.se/~sasha/SLipids/Downloads.html)

• Special purpose super-computer

  • MD-GRAPE(http://www.qbic.riken.jp/japanese/research/outline/lab-09.html)
  • ANTON(https://www.psc.edu/resources/computing/anton)

• Analysis tools

  • MDToolbox(http://mdtoolbox.readthedocs.io/en/latest/)
  • cpptraj(http://ambermd.org/AmberTools.php)
  • MMTSB(http://www.mmtsb.org)
  • MDTraj(http://mdtraj.org/)
  • MDAnalysis(https://www.mdanalysis.org/)
  • Wordom(https://sourceforge.net/projects/wordom/)
  • ProDy(http://prody.csb.pitt.edu)

• Visualization tools

  • VMD(http://www.ks.uiuc.edu/Research/vmd/)
  • PyMol(https://pymol.org/)
  • UCSF CHIMERA(https://www.cgl.ucsf.edu/chimera/)
  • LIGPLOT(https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/)

• MD tutorials

  • GENESIS(http://www.aics.riken.jp/labs/cbrt/tutorial/)
  • CHARMM(https://www.charmmtutorial.org/index.php/Outline)
  • AMBER(http://ambermd.org/tutorials/)
  • GROMACS(http://www.gromacs.org/Documentation/Tutorials)

• Web server

  • PROPKA(http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/)
  • CHARMM-GUI(http://www.charmm-gui.org)
  • PREDDIMER(http://model.nmr.ru/preddimer/)
  • DynDom(http://fizz.cmp.uea.ac.uk/dyndom/)

• Database

  • Orientation of proteins in membranes(http://opm.phar.umich.edu)
  • PDBTM(http://pdbtm.enzim.hu/)

• Simulation movies (YouTube)

  • All-atom Molecular Dynamics Simulation of the Bacterial Cytoplasm(https://www.youtube.com/watch?v=5JcFgj2gHx8)

Bioinformatics

• Software

  • Clustal(http://www.clustal.org/)
  • ROSETTA(https://www.rosettacommons.org)

• Database

  • UniProt(http://www.uniprot.org/)
  • CATH(http://www.cathdb.info/)
  • Pfam(http://pfam.xfam.org/)