X-ray:

• Crystal Resource:  http://xtal.uvm.edu/
• X-ray Software Resource:  http://www.xray.utmb.edu/xray_software.htm
• CCP4:  http://www.ccp4.ac.uk/
• Phenix:  http://www.phenix-online.org/
• CNS:  http://cns-online.org/v1.3/
• Uppsala Software Factory:  http://xray.bmc.uu.se/usf/
• HKL2000&3000:  http://www.hkl-xray.com/
• MOSFLM:  http://www.mrc-lmb.cam.ac.uk/harry/mosflm/
• SCALA:  http://www.ccp4.ac.uk/html/scala.html
• TRUNCATE:  http://www.ccp4.ac.uk/html/truncate.html
• Twin detection:  http://services.mbi.ucla.edu/Twinning/
• DETWIN:  http://www.ccp4.ac.uk/dist/html/detwin.html
• Phaser:  http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software
• MOLREP:  http://www.ysbl.york.ac.uk/~alexei/molrep.html
• SHARP & AutoSHARP:  http://www.globalphasing.com/sharp/
• SOLVE & RESOLVE:  https://solve.lanl.gov/index.html
• SHELX:  http://shelx.uni-ac.gwdg.de/SHELX/
• ARP/wARP:  http://www.embl-hamburg.de/ARP/
• TLS Motion Determination:  http://skuld.bmsc.washington.edu/~tlsmd/
• PRODRG:  http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg
• JLigand:  http://www.ysbl.york.ac.uk/mxstat/JLigand/

NMR:

General NMR knowledge:

• NMR Wiki:  http://nmrwiki.org/wiki/index.php?title=Main_Page
• BioNMR:  http://www.bionmr.com/
• NMR Wiki:  http://nmrwiki.org/wiki/index.php?title=Main_Page
• Protein NMR:  http://www.protein-nmr.org.uk/
• NMR Wiki software:  http://nmrwiki.org/wiki/index.php?title=NMR_Software
• NMR software link:  http://www.cgl.ucsf.edu/home/sparky/nmrlinks.html
• NMRPipe:  http://spin.niddk.nih.gov/NMRPipe/
• Sparky:  http://www.cgl.ucsf.edu/home/sparky/
• CARA:  http://cara.nmr-software.org/portal/
• ARIA:  http://aria.pasteur.fr/
• CCPN:  http://www.ccpn.ac.uk/
• CNS:  http://cns-online.org/v1.3/
• Cyana:  http://www.cyana.org/wiki/index.php/Main_Page
• TALOS:  http://spin.niddk.nih.gov/bax/software/TALOS/
• HADDOCK:  http://www.nmr.chem.uu.nl/haddock/
• CS-ROSETTA:  http://spin.niddk.nih.gov/bax/software/CSROSETTA/
• Relax:  http://www.nmr-relax.com/
• ModelFree:  http://www.palmer.hs.columbia.edu/software/modelfree.html
• DASHA:  http://www.nmr.ru/dasha.html
• PALES:  http://spin.niddk.nih.gov/bax/software/PALES/
• Module 2:  http://www.ibs.fr/science-213/scientific-output/software/module/?lang=en
• PROCHECK-NMR:  http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/
• SpinCore products:  http://spincore.com/nmrinfo/

Docking & Modeling:

• AutoDock:  http://autodock.scripps.edu/
• ZDOCK:  http://zlab.umassmed.edu/zdock/index.shtml
• GRAMM-X:  http://vakser.bioinformatics.ku.edu/resources/gramm/grammx
• YASARA:  http://www.yasara.org/minimizationserver.htm
• Rosetta:  https://www.rosettacommons.org/
• MODELLER:  http://salilab.org/modeller/modeller.html
• SWISS-MODEL:  http://swissmodel.expasy.org//SWISS-MODEL.html

Structure Analysis:

• Coot:  http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/
• Pymol:  http://www.pymol.org/
• VMD:  http://www.ks.uiuc.edu/Research/vmd/
• MolMol:  http://www.msg.ucsf.edu/local/programs/molmol/manual.html
• Molprobity:  http://molprobity.biochem.duke.edu/
• What Check:  http://swift.cmbi.ru.nl/gv/whatcheck/
• Dali:  http://ekhidna.biocenter.helsinki.fi/dali_server/
• PDBePISA:  http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
• The ConSurf Server:  http://consurf.tau.ac.il/
• Electron Density Server:  http://eds.bmc.uu.se/eds/
• PDB2PQR:  http://nbcr-222.ucsd.edu/pdb2pqr_1.8/
• APBS:  http://www.pymolwiki.org/index.php/APBS
• LIGPLOT:  http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT