リンク集

• クライオ電顕(Cryo-EM)
• 核磁気共鳴分光法 (NMR)
• X線結晶構造解析 (X-ray crystallography)
• X線小角散乱 (Small angle X-ray scattering)
• 分子動力学計算(MD)
• バイオインフォマティクス

本リンク集は、各サブ課題で用いる手法（クライオ電顕、核磁気共鳴分光法、分子動力学計算など）において、よく利用されているソフトウェア、データベース、ウェブツール、解説記事などをまとめており、異分野の研究者が各分野の手法に関する情報を効率よく収集し、分野融合、交流、知識の共有を促すことを目的としています。

クライオ電顕(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/)

核磁気共鳴分光法 (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線結晶構造解析 (X-ray crystallography)

• 大型放射光施設

  • 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)

X線小角散乱 (Small angle X-ray scattering)

• 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)

分子動力学計算(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)

バイオインフォマティクス

• 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/)