YASARA

Yet Another Scientific Artificial Reality Application (YASARA) is a computer program for molecular visualising, modelling, and dynamics. It has many scientific uses, as expressed by the large number of scientific articles mentioning the software.^[1] The free version of YASARA^[2] is well suited to bioinformatics education. A series of freely available bioinformatics courses exist that use this software.

See the Center for Molecular and Biomolecular Informatics (CMBI) education pages for a series of examples.^[3]

• "Increasing the precision of comparative models with YASARA NOVA—a self-parameterizing force field". Proteins 47 (3): 393–402. May 2002. doi:10.1002/prot.10104. PMID 11948792. 
• Modelling:
  "Models@Home: distributed computing in bioinformatics using a screensaver based approach". Bioinformatics 18 (2): 315–8. Feb 2002. doi:10.1093/bioinformatics/18.2.315. PMID 11847079. http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=11847079. 
• Dynamics:
  "Making optimal use of empirical energy functions: force-field parameterization in crystal space". Proteins 57 (4): 678–83. Dec 2004. doi:10.1002/prot.20251. PMID 15390263. 

• List of molecular graphics systems
• Comparison of software for molecular mechanics modeling
• Molecular graphics
• Molecular design software

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