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Pknot DataBase Notes

July 18, 2010

Location: http://www.rnaparse.com/database/menu.php

All data is freely available for research. Please cite: RNAParse.com James F. Lynn.

The database is very recently built (July 2009) and updated frequently with new material. Selected short pknots from the pseudobase site are included and renamed with a RP#0000 due to convention (See notes section of the database for credits and additional information.)

Convert all U to T where applicable.

Bio-computational pseudoknots may or may not exist in nature. The purpose of this database is to help determine the specific properties that natural pseudoknots possess. Thus, the computational methods used to discover new structures entered here are “possibility” structures and may or may not have gone further filtering via energy methods.

Structures that pass or fail energy models are denoted in the notes portion of the databases as: KSPOS or KSNEG, meaning they have passed “knot seeker” criteria for actually being pseudoknots. A separate database holds pknots that have been ran through a grammatic filter to match lowest energy structures, i.e. those more likely found in nature.

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