Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.

By Yuanpeng Janet Huang, Robert Powers, Gaetano T. Montelione. 2005

265 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. R. Tejero
2. Gaetano T. Montelione
3. T. Ramelot
4. Yuanpeng Janet Huang
5. David Baker
6. Ivan V. Anishchenko
7. Sergey Ovchinnikov
8. Binchen Mao

In Materials Chemistry

1. David Baker
2. Gaetano T. Montelione
3. Sergey Ovchinnikov
4. Frank DiMaio
5. Ivan V. Anishchenko
6. Yuanpeng Janet Huang
7. Binchen Mao
8. R. Tejero

In Molecular Biology

1. Gaetano T. Montelione
2. David Baker
3. Sergey Ovchinnikov
4. Frank DiMaio
5. Ivan V. Anishchenko
6. Yuanpeng Janet Huang
7. Binchen Mao
8. R. Tejero

Citations in the corpus

• De novo protein design by deep network hallucination (2020, methodology): “NOESY peak assignments were made automatically using Cyana 46,47 , together with the programs RPF and ASDP to guide manual correction of NOESY peak assignments 48,49 .”
• NMR-assisted protein structure prediction with MELDxMD (2019, methodology): “Then ASDP (Automated Structure Determination of Proteins), software designed for automatic assignment of NOESY data, 12,13 was used to generate the ambiguous contact tables that contained possible atom-atom contacts for each peak.”
• Assessment of template based protein structure predictions in CASP10 (2014, methodology): “25,28 For this reason, RPF-9 DP scores used in CASP10 are very discriminative against random structures.”
• A topology‐constrained distance network algorithm for protein structure determination from NOESY data (2005, unknown): “[15-22] This program also plays a central role in the NMR structure analysis component of the Northeast Structural Genomics Consortium ( http://www.”
• Evaluating protein structures determined by structural genomics consortia (2006, methodology): “Validation must also include assessments of how well the structure satisfies the experimental data from which it is derived, such as crystallographic R-factors, NMR RPF scores, 15 and constraint violation analyses.”
• AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures (2022, methodology): “The RPF-DP score algorithm is outlined schematically in Figure 1, adopted from Huang et al (Huang et al., 2005; Huang et al., 2012; Huang et al., 2021).”
• Protein structure determination by combining sparse NMR data with evolutionary couplings (2015, unknown): “The NMR RPF Recall score measures the fraction of NOESY cross peaks that can be explained by the decoy model structure.”
• Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, background): “The NESG consortium, involving several NMRgroups, has focused efforts on improving the efficiency and accuracy of its NMR structure determination pipeline, and has implemented strict quality control measures to ensure the production of high-quality structures (Kim and Szyperski, 2003; Huang et al., ”
• RPF: a quality assessment tool for protein NMR structures (2012, methodology): “In general, an accurateNMR-derived protein structure should score well in all of these different and complementary views of structure quality (3).”
• Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2 (2021, unknown): “0).(15) Accurate structures generally have DP for individual models > 0.”