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huangy26 authored Oct 3, 2023
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Expand Up @@ -15,17 +15,17 @@ ASDP generates distance constraint lists and utilizes the programs CYANA, or Xpl
The ASDP protocol, in principle, resembles the method that an expert would utilize in manually solving a protein structure by NMR. ASDP "bottom up" strategy is quite different from the "top down" strategies used by programs CANDID and ARIA, which rely on "ambiguous constraints". For NOESY spectra with poor signal-to-noise ratios, such automatically assigned "ambiguous constraints" sets may not include any true NOESY assignments, and result in small distortions of the protein structure which may be avoided by the "bottom up" approach of ASDP. CANDID/CYANA also uses a "network anchoring" approach similar to, but less comprehensive than, the topology-constrained approach used by ASDP. For these reasons, some users may prefer to use both ASDP and CANDID/CYANA or ARIA in parallel to assess potential errors in automated NOESY cross peak assignments.


### For citing ASDP you may consider:
#### For citing ASDP you may consider:

Huang, Y. J.; Tejero, R.; Powers, R.; Montelione, G.T. A topology-constrained distance network algorithm for protein structure determination from NOESY data. PROTEINS: Struct. Funct. Bioinformatics 15, 587-603 (2006)

Huang, Y.J., Mao, B., Xu, F., and Montelione, G.T. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score. J. Biomol. NMR, 62: 439-451, 2015.

# RPF ReadMe
### RPF/DP

RPF uses a novel, rapid, and simple approach for calculating global NMR structure quality scores. This program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power(DP) scores, which estimate the difference in F-MEASURE scores between the query structure and "random coil" structures, as an indictor of the correctness of the overall fold.

### For citing RPF you may consider:
#### For citing RPF you may consider:

Huang, Y. J.; Powers, R. & Montelione, G. T. Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127, 1665-74 (2005)

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