DNA & RNA Structure and Helical Parameters Analyses (NAFlex)
Tutorial 1 -- Search
Tutorial 2 -- Global analysis (XCGY)
Tutorial 3 -- Meta-trajectory (XCGY)
Tutorial 4 -- Experimental vs MD analysis
A strong requirement to organize any knowledge field is the agreement in the terminology used. This has been a concern in Bioinformatics and has led to the development of a number of ontologies describing several aspects of the discipline (see J. Ison et al., Bioinformatics, 29, 1325-1332., M. Ashburner et al, Nature Genetics, 25, 25-29., or J. Hastings et al, NAR, 41, D456-D463).
Here we have developed a partial ontology to describe Nucleic Acids simulations. The contents of such ontology is used to qualify simulations, and power the search facility. Simulation browser tables (see browsing section of this help), and simulation details (see simulation section of this help) include the set of keywords derived from the ontology.
In its present state, the generated Nucleic Acids ontology represents merely a set of normalized terms, but it is being fully developed in a separate project and will be documented elsewhere.
Nucleic Acids Ontology Navigation