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Citations per year

Number of citations per year for the bioinformatics software tool Afree

Tool usage distribution map

This map represents all the scientific publications referring to Afree per scientific context
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Associated diseases


Popular tool citations

chevron_left Amino acid sequence homology search Gene orthology prediction Nucleotide sequence homology search chevron_right
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Afree specifications


Unique identifier OMICS_23577
Name Afree
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Two formated proteome files.
Input format FASTA+FASTA
Output data A table of pairwise similarities.
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 2.0
Stability Beta
Maintained No




No version available


This tool is not maintained anymore.

Afree citations


Detecting stoichiometry of macromolecular complexes in live cells using FRET

Nat Commun
PMCID: 5150656
PMID: 27922011
DOI: 10.1038/ncomms13709

[…] revealed a saturating binding relation as previously reported (; ). Similarly, E-FRET efficiency (ED) also followed a saturating binding isotherm against the concentration of free acceptor molecules (Afree) (). Remarkably, under these conditions EA,max approximately equalled to ED,max. Of note, CFP-fused CaM does not associate with membrane tethered EYFP (). Computing the stoichiometry ratio, ν=1. […]


Studies of IscR reveal a unique mechanism for metal dependent regulation of DNA binding specificity

PMCID: 3676455
PMID: 23644595
DOI: 10.1038/nsmb.2568
call_split See protocol

[…] bient light, a 10 second delay prior to reading was used. When saturated binding to the labeled DNA was achieved, a four parameter Hill equation was used to fit the data (SigmaPlot version 12.0): A = Afree + ((Abound−Afree)[IscR]n)/(Kdn+[IscR]n)] in which A is the anisotropy, Afree is the anisotropy of unbound DNA, Abound is the anisotropy under saturating binding conditions, [IscR] is the concent […]


Efficient large scale protein sequence comparison and gene matching to identify orthologs and co orthologs

Nucleic Acids Res
PMCID: 3315314
PMID: 22210858
DOI: 10.1093/nar/gkr1261

[…] logs’ section). Five comparisons, as described in the previous paragraph, were performed with initial sequence similarity data attained from BLAST (denoted as EGMB ), UBLAST (denoted as EGMU) and the afree (denoted as EGMAF) approach. Note that UBLAST50 was not used as the aim of this experiment is to identify the maximum number of orthologs and further, UBLAST50 ⊆ UBLAST. We used the EnsEMBL Comp […]


The past, present and future of Scientific discourse

J Cheminform
PMCID: 3208583
PMID: 21999632
DOI: 10.1186/1758-2946-3-46

[…] rections are computed for geometries optimized at the ωB97XD/6-311G(d, p) level with application of a SCRF solvent continuum field for water. The display coordinates are those obtained at this level. aFree energy for the dimerisation of a single strand to a duplex.Armed with optimized coordinates which include the weaker interactions between atoms one can annotate the basic models revealed in Figu […]


A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

PLoS Comput Biol
PMCID: 3102756
PMID: 21637799
DOI: 10.1371/journal.pcbi.1002054

[…] To compute the binding free energy ΔG from our simulations, we use the method introduced by van Gunsteren and co-workers : (3)where αbound and αfree are the fractions of bound and free species respectively. c0 is the overall concentration of ligand. In our simulations, , where NA is Avogadro's number, and Vbox is the volume of the simulation […]


The DNA binding CXC domain of MSL2 is required for faithful targeting the Dosage Compensation Complex to the X chromosome

Nucleic Acids Res
PMCID: 2879509
PMID: 20139418
DOI: 10.1093/nar/gkq026

[…] of AB and KD is the affinity constant. For competition experiments, first AB was calculated from the difference between the signal of total nucleic acid (Atotal) and the signal of free nucleic acid (Afree). Then the fraction bound was calculated (AB/Atotal) and normalized to the fraction bound measured at 0 nM competitor. Competition curves were obtained with the following competition model: , wh […]

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