ArticleJournal of biomolecular NMR2000
RFAC, a program for automated NMR R-factor estimation.
Article in Journal of biomolecular NMR, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A method for validating the accuracy of NMR protein structures.Nature communications · 2020Article
- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
- Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.Journal of biomolecular NMR · 2012Article
- Structure-oriented methods for protein NMR data analysis.Progress in nuclear magnetic resonance spectroscopy · 2010Review
- Protein structure calculation with data imputation: the use of substitute restraints.Journal of biomolecular NMR · 2009Article
- Article
- Chemical shift optimization in multidimensional NMR spectra by AUREMOL-SHIFTOPT.Journal of biomolecular NMR · 2009Article
- AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures.Journal of biomolecular NMR · 2007Article
- A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm.BMC structural biology · 2006Article
- Weighting of experimental evidence in macromolecular structure determination.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Traditional biomolecular structure determination by NMR spectroscopy allows for major errors.PLoS computational biology · 2006Article
- A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles.BMC bioinformatics · 2005Article
- Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling, transverse relaxation and chemical shift anisotrophy.Journal of biomolecular NMR · 2004Article
- High-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus and characterization of its interaction with the bifunctional HPr kinase/phosphorylase.Journal of bacteriology · 2004Article
- High-temperature solution NMR structure of TmCsp.Protein science : a publication of the Protein Society · 2004Article
- Rapid protein fold determination using unassigned NMR data.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.Journal of biomolecular NMR · 2002Article
- Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).Journal of biomolecular NMR · 2002Article
- An NMR approach to structural proteomics.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
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7 authors.
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Abstract
A computer program (RFAC) has been developed, which allows the automated estimation of residual indices (R-factors) for protein NMR structures and gives a reliable measure for the quality of the structures. The R-factor calculation is based on the comparison of experimental and simulated 1H NOESY NMR spectra. The approach comprises an automatic peak picking and a Bayesian analysis of the data, followed by an automated structure based assignment of the NOESY spectra and the calculation of the R-factor. The major difference to previously published R-factor definitions is that we take the non-assigned experimental peaks into account as well. The number and the intensities of the non-assigned signals are an important measure for the quality of an NMR structure. It turns out that for different problems optimally adapted R-factors should be used which are defined in the paper. The program allows to compute a global R-factor, different R-factors for the intra residual NOEs, the inter residual NOEs, sequential NOEs, medium range NOEs and long range NOEs. Furthermore, R-factors can be calculated for various user defined parts of the molecule or it is possible to obtain a residue-by-residue R-factor. Another possibility is to sort the R-factors according to their corresponding distances. The summary of all these different R-factors should allow the user to judge the structure in detail. The new program has been successfully tested on two medium sized proteins, the cold shock protein (TmCsp) from Termotoga maritima and the histidine containing protein (HPr) from Staphylococcus carnosus. A comparison with a previously published R-factor definition shows that our approach is more sensitive to errors in the calculated structure.
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