# NAPSS Benchmark folder
# Author: Richard M. Watson (2017)

This directory (napss/benchmark) contains reference sequences, NMR constraints, and output (ct and pp files) 
for the NAPSS program.

Specifically:
For each sequence (e.g. adhr1) there exists:
1. A sequence file, e.g.: adhr1.seq
2. An NMR constraints file using triplet constraints, e.g.: adhr1.con
3. An "accepted" literature reference structure: adhr1.LIT.ct
4. The NAPSS output and results that were published in the 2015 Biochemistry article (reference below)
	(a) Structure (CT) output file: adhr1.PUB.ct
	(b) Output from `scorer` when comparing the NAPSS output CT to the literature structure: adhr1.PUB.score
	(c) Standard output from the NAPSS program: adhr1.PUB.stdout  (useful for debugging future regressions)

Publication with NAPSS results: 
	Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints
	Jonathan L. Chen, Stanislav Bellaousov, Jason D. Tubbs, Scott D. Kennedy, Michael J. Lopez, David H. Mathews, and Douglas H. Turner
	Biochemistry 2015, 54, 6769-6782		DOI: 10.1021/acs.biochem.5b00833

In addition there is a file "scores.PUB.txt" that contains a summary of scores for all reference sequences.

The file "run-bench" is a bash script that can be executed to run NAPSS on all reference input (seq and con files) 
and produce benchmark output in a subdirectory of the napss/benchmark folder 
(by default this is napss/benchmark/out but it can be changed using the -d option to the script). 
The script also runs scorer on all output and creates a summary file "scores.BENCH.txt" of all generated output 
scores and finally compares this against the published values ("scores.PUB.txt").

List of Sequences: (TODO: Add scientific names.)
adhr1
bm
bm_ml
domain1
har1
hdv2
mdCR45
mlv
pbuE
pemv1
pk1
seg7mbl
spn
srv1mut
srv1wt
tRNATrpBacillus
tRNATrpBovine
vpk
