fmcsR specifications

Information


Unique identifier OMICS_23119
Name fmcsR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License Artistic License version 2.0
Computer skills Advanced
Version 1.23.2
Stability Stable
Requirements
R(>=2.10.0), methods, parallel, BiocGenerics, BiocStyle, RUnit, knitr, ChemmineR, knitcitations, knitrBootstrap
Maintained Yes

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Maintainer


  • person_outline Thomas Girke <>

Publication for fmcsR

fmcsR in publications

 (3)
PMCID: 5767195
PMID: 28831657
DOI: 10.1007/s10822-017-0049-y

[…] accuracy in generating near-native poses (see “” section). accordingly, we identified the ligand that is most similar to fxr1-36 for targets fxr37-102 based on the tanimoto distance calculated using fmcsr [] and chemminer packages []. the corresponding receptor conformation was used as the protein input for all docking runs in stage2., as for input ligand ensemble, we followed the stage1 […]

PMCID: 4912613
PMID: 27301419
DOI: 10.1038/ncomms11901

[…] using the flexible mcs (fmcs) finder package in r. clustering was conducted using hclust with a ward.d2 method setting. pairwise distances were calculated between tanimoto coefficient values from fmcsr., p. falciparum parent strains 3d7 and dd2 used for selection were obtained from the labs of dan goldberg and david fidock, respectively. the fidock lab additionally supplied the dd2δexo strain […]

PMCID: 4890880
PMID: 27275010
DOI: 10.1021/acsinfecdis.5b00143

[…] imaging assay. briefly, smilesl (simplified molecular-input line-entry system) strings were loaded into r, and the maximum common substructure tanimoto coefficient (mcs-tc) was calculated using the fmcsr package. the compounds were then subsequently hierarchically clustered with the hclust package, using the ward.d2 agglomeration method pair clusters. to create compound bins, the tree branches […]


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fmcsR institution(s)
Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
fmcsR funding source(s)
Supported by the National Science Foundation (ABI-0957099 and IGERT-0504249).

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