RPF protocols

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RPF specifications

Information


Unique identifier OMICS_19958
Name RPF
Alternative name Recall Precision F-measure
Interface Web user interface
Restrictions to use None
Input data The atomic coordinate files, chemical shift data and NOESY peak lists.
Input format PDB, BMRB, Sparky, Xeasy
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Gaetano Montelione <>
  • person_outline RPF Team <>

Publications for Recall Precision F-measure

RPF in pipeline

2015
PMCID: 4521990
PMID: 26121406
DOI: 10.1038/nmeth.3455

[…] x-ray crystal or nmr structure is the “ground truth”, and the ec or rpc contacts are the “prediction”. they differ from those used in assessing nmr models against nmr noesy peak list data (nmr rpf), in which the model is taken as the “prediction” and the noesy data is the “ground truth”., backbone (defined as n, cα, c’, and o atoms) and all-heavy-atom (n, c, o, s) root mean square […]


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RPF in publications

 (11)
PMCID: 5533445
PMID: 28753623
DOI: 10.1371/journal.pone.0181551

[…] including global quality factor from verify 3d, prosaii, procheck [] and molprobity []. the global goodness-of-fit of the final structure ensemble of the noesy peak list data was calculated using rpf analysis []., the chemical shift index (csi) of backbone atoms can be used to identify the secondary structural elements of a specific protein []. the csi of cβ and nh atoms provides a prediction […]

PMCID: 5385502
PMID: 28393921
DOI: 10.1038/srep45863

[…] ensemble of sc16 consists of the 20 lowest energy structures out of 200. these structures were refined in water by cns 1.21. the quality of the final ensemble of structures was assessed through rpf analysis, procheck and the psvs suite. the pymol molecular graphics system (version 1.7.1 schrödinger, llc) was used for visualization, distance measurements, and figure generation. chemical […]

PMCID: 4521990
PMID: 26121406
DOI: 10.1038/nmeth.3455

[…] it has been demonstrated that accurate conventional nmr structures have z scores more positive than z = −2 to −3 for these structure quality assessment metrics. other useful validation metrics are rpf-dp scores, which compare models against the unassigned noesy data and resonance assignments,. rpf-dp scores are correlated with structure accuracy for fully- protonated proteins, with reliable […]

PMCID: 4569653
PMID: 26032236
DOI: 10.1007/s10858-015-9949-0

[…] clashes was performed using the psvs (bhattacharya et al. ) server (http://psvs-1_5-dev.nesg.org/). psvs integrates analyses from several widely-used structure quality evaluation tools, including rpf (huang et al. ), procheck (laskowski et al. ), procheck_nmr (laskowski et al. ), ramachandran (lovell et al. ), verify3d (lüthy et al. ), prosa ii (sippl ) and probe (word et al. ). for the dp […]

PMCID: 4477651
PMID: 25969444
DOI: 10.1093/nar/gkv410

[…] the program cns in explicit solvent (). validation of the resulting ensemble of structures was performed using the protein structure validation server (psvs) (,) and recall, precision, f-measure (rpf) analysis of the agreement between structural models and noesy peak list data (). ‘promals3d’ was used for generating structure-based sequence alignments of the pfv, hiv and mlv ctd structures […]


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RPF institution(s)
Center for Advanced Biotechnology and Medicine, Northeast Structural Genomic Consortium, Rutgers University, Piscataway, NJ, USA; Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy; Robert Wood Johnson Medical School, University of Medicine and Dentistry of NJ, Piscataway, NJ, USA
RPF funding source(s)
Supported by Protein Structure Initiative of the National Institutes of Health [U54-GM094597]; the European Community FP7 e-Infrastructure ‘WeNMR’ projects [261572].

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