RFMQA specifications

Information


Unique identifier OMICS_18587
Name RFMQA
Alternative name Random Forest-Based Protein Model Quality Assessment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://lee.kias.re.kr/RFMQA/RFMQA_eval.tar.gz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jooyoung Lee

Publication for Random Forest-Based Protein Model Quality Assessment

RFMQA citations

 (2)
library_books

Sorting protein decoys by machine learning to rank

2016
Sci Rep
PMCID: 4987638
PMID: 27530967
DOI: 10.1038/srep31571

[…] uctural element (alpha-helix, beta-strand and coil) between the DSSP label and the PSIPRED output is calculated by dividing the consistency number by its total chain length, and the total consistency RFMQA-SS-total score is also used as a feature. For solvent accessibility features, the absolute solvent accessibility of the model is computed by DSSP and relative solvent accessibility is computed b […]

library_books

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

2016
PLoS One
PMCID: 4720428
PMID: 26790000
DOI: 10.1371/journal.pone.0147240

[…] DB). The missing residues (87–89) in the linker region of the Oct4 crystal structure were built into the Oct4/PORE/DNA structure, as described previously [], and a final model was chosen based on the random forest-based protein model quality assessment (RFMQA) score []. The homologous Oct1 and Oct4 transcription factors possess similar DNA-binding specificities []. Hence, we modeled these two comp […]

RFMQA institution(s)
Center for In Silico Protein Science, School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
RFMQA funding source(s)
Supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (No. 2008-0061987).

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