Yasara

YASARA (acronym of Yet Another Scientific Artificial Reality Application) is a molecular visualisation, modelling, and dynamics program that can be used for a series of scientific applications as is expressed by the large number of scientific articles mentioning this software. The free version of YASARA (YASARA-View) is well suited for bioinformatics education. A series of freely available bioinformatics courses exist that use this software.

Students working on an educational task using YASARA.

See the CMBI education pages for a series of examples.

• Krieger E, Koraimann G, Vriend G (May 2002). "Increasing the precision of comparative models with YASARA NOVA—a self-parameterizing force field". Proteins 47 (3): 393–402. doi:10.1002/prot.10104. PMID 11948792. 

• Modelling:
  Krieger E, Vriend G (Feb 2002). "Models@Home: distributed computing in bioinformatics using a screensaver based approach". Bioinformatics 18 (2): 315–8. doi:10.1093/bioinformatics/18.2.315. PMID 11847079. 

• Dynamics:
  Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G (Dec 2004). "Making optimal use of empirical energy functions: force-field parameterization in crystal space". Proteins 57 (4): 678–83. doi:10.1002/prot.20251. PMID 15390263. 

Learning to dock ligands with YASARA.

See also

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