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RF-Score specifications

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Unique identifier OMICS_19899
Name RF-Score
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for RF-Score

RF-Score in publications

 (34)
PMCID: 5947827
PMID: 29412457
DOI: 10.1002/path.5051

[…] cms class (i.e. a sample will have a score for cms1, cms2, cms3, and cms4) before a final classification is made. using these individual cms scores, we created a cms ratio based on the change in rf score, from ct and if regions, for each patient‐matched sample (figure a). we demonstrated an increase in the relative classification score for cms1 and 4 subtypes (the stromal subtypes) […]

PMCID: 5871981
PMID: 29538331
DOI: 10.3390/biom8010012

[…] learning instead of the classical linear regression approach of the fourth sf (x-score which has the best test set performance out of 16 classical sfs). we have found that random forest (rf)-based rf-score-v3 outperforms x-score even when 68% of the most similar proteins are removed from the training set. in addition, unlike x-score, rf-score-v3 is able to keep learning with an increasing […]

PMCID: 5740072
PMID: 29269744
DOI: 10.1038/s41598-017-18178-0

[…] therefore, pi3kα appears to be an ideal target for drug development. in this study, we utilized free and open-source protein-ligand docking software idock,, binding affinity prediction software rf-score-v3, and molecular visualization tool iview to screen 3167 fda-approved small molecules to identify putative pi3kα inhibitors. among them, econazole nitrate, an antifungal agent, exhibited […]

PMCID: 5712561
PMID: 29238696
DOI: 10.3389/fonc.2017.00288

[…] be most likely closest to the crystal pose ()., following docking, the compounds were sorted in ascending order of their predicted binding free energy. meanwhile, the more accurate scoring function rf-score v3 was executed to rescore all the compounds (), providing an additional and more reliable estimation of intermolecular binding strength, given the assumption that the compounds […]

PMCID: 5705913
PMID: 29184023
DOI: 10.1128/mBio.01050-17

[…] mutations with a frequency of <0.01% in the transfection library were filtered out, and possible g-a hypermutations were removed (). lethal mutations were defined as the mutations with log10(rf score) of less than −0.95. that value represented the distribution peak of nonsense mutations, while only 2.5% of synonymous mutations fell below this cutoff., a total of 6,097 prealigned hiv-1 […]


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RF-Score institution(s)
Department of Computer Science and Engineering, Chinese University of Hong Kong, Hong Kong, China; Cancer Research Center of Marseille, INSERM U1068, Marseille, France; Institut Paoli-Calmettes, Marseille, France; Aix-Marseille Université, Marseille, France; CNRS UMR7258, Marseille, France
RF-Score funding source(s)
Supported by the A*MIDEX grant (n° ANR-11-IDEX-0001-02) funded by the French Government “Investissements d’Avenir” program, the Direct Grant from the Chinese University of Hong Kong and the GRF Grant (Project Reference 414413) from the Research Grants Council of Hong Kong SAR. Publication of this article was funded by the Direct Grant from the Chinese University of Hong Kong and the GRF Grant (Project Reference 414413) from the Research Grants Council of Hong Kong SAR.

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