Fluorescence resonance energy transfert data analysis software tools
Förster (or Fluorescence) Resonance Energy Transfer (FRET) is unique in generating fluorescence signals sensitive to molecular conformation, association, and separation in the 1-10 nm range. […] Applications extending from a single molecule to live cells will benefit from multidimensional microscopy techniques, particularly those adapted for optical sectioning and incorporating new algorithms for resolving the component contributions to images of complex molecular systems.
Offers an application dedicated to single-molecule fluorescence resonance energy transfer (SmFRET) with total-internal-reflection fluorescence (TIRF)-microscopy data analyses. iSMS provides features including molecule localization, detection of bleaching, FRET distribution as well as molecule subpopulation analysis. Additionally, it also proposes functions for generating figures for further publishing and utilities for visualization of the performed data.
Allows users to perform simulation and analysis of forster resonance energy transfer (FRET) in nucleic acids. FRETmatrix is based on a matrix base-centred calculation scheme to build nucleic acid geometries. Moreover, this program can be used, in combination with base–base FRET, for reconstructing the 3D structure of local kinks, such as protein/ligand binding sites, bulges, junctions and DNA lesions.
Allows users to identify nucleic acid–protein interactions in plant leaves. The Taupography method uses fluorescence resonance energy transfer (FRET) approach to detect theses interactions. Also, this tool utilizes fluorescence lifetime imaging microscopy (FLIM) to work about this topic. It identifies proteins of interest (POI) thanks to a Green Fluorescent Protein (GFP) and transiently expressed in plant cells to serve as donor fluorophor.
Analyzes single molecule time trajectories that display dynamic disorder. VB-DCMM allows to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformation al transition within each internal state. VB-DCMM allows to decompose individual H-DNA time traces with dynamic disorder into multiple components, each of which should satisfies the property of homogeneous Markov chain.
Calculates fluorescence (or Förster) resonance energy transfer (FRET) between fluorophores distributed in any geometry. ExiFRET extends the Monte Carlo calculation scheme that allows calculation of the efficiency of energy transfer between multiple fluorophores, either in ensembles or attached to single molecules. The software has been used to predict the efficiency for fluorophores randomly distributed in two and three dimensions linked in donor-acceptor pairs with excluded volumes, and linked in pentamers.
Enables platform-independent analysis of Fluorescence resonance energy transfer (FRET) by acceptor photo-bleaching. FRETcalc implements the FRETTH algorithm, that is based on pixel selection and pixel-to-pixel analysis of the experimental images. The software is applicable for FRET estimation in organelles with non-continuous and continuous shapes, as well as for non-protein fluorophores. The output options include histograms and plots of the donor, acceptor, and FRET intensities in the analyzed region of interests (ROIs).
Allows users to calculate and display fluorescence resonance energy transfer (FRET) directly on images. PixFRET permits computation by performing a pixel-by-pixel analysis of images and assisting in the determination of spectral bleed-throughs (SBTs). It also assists in the determination of SBT parameters and the display of normalized FRET images.
Determines the approximate space in which the dye is able to move. Available Volume is a method for potentially replacing molecular dynamics (MD) simulations in Förster resonance energy transfer FRET data interpretation. The software calculates the volume accessible for dye movement using a geometrical algorithm. An accurate Available Volume calculation requires a good random distribution of the orientation of the linker elements.
Identifies all conformational states of dyes and overlays these on the macromolecular system using preliminary molecular dynamics (MD) simulations of fluorescent dyes in solution. Free Dye snapshots is a method for potentially replacing molecular dynamics (MD) simulations in Förster resonance energy transfer FRET data interpretation. The software allows explicit calculations of dyes positions and orientation.
Provides information about relative orientations and favorable dyes conformations. Rotamer Library is a method for potentially replacing molecular dynamics (MD) simulations in Förster resonance energy transfer FRET data interpretation. The method was adapted from the analysis of electron paramagnetic studies and utilizes a library of rotamers describing probe conformations.
Automates processing of intensity-based cell image segmentation. FLIM-FRET analyzer can separate objects of interest from the background to delineate whole cells. It simplifies image segmentation into single cells followed by donor lifetime and donor/acceptor fluorescence intensity quantification. For the software to work, users have to create a FRET collection which associates fluorescent intensity and fluorescence decay image datasets. To create a FRET collection, users import the donor and acceptor fluorescent channels and the donor fluorescence decay curves.
Represents an integrated solution for data analysis and acquisition. SymPhoTime 64 permits users to target principally the results rather than the data processing. The interface of this tool simplifies the utilization by the user for an individual analysis or measurement process. Different data acquisition modes including interleaved trains of excitation and stimulated emission depletion (STED) laser pulses are integrated in a graphical user interface (GUI).
Assists users to perform fluorescence decay analysis. DecayFit is a program that includes several features allowing researchers to execute several works: analyze time-resolved fluorescence decays by iterative reconvolution or modified tail fitting; global optimization: analysis of multiple decays simultaneously; time-resolved forster resonance energy transfer (FRET) analysis; or parameter confidence interval estimation.
Manages instrument control, image processing and data analysis. SlideBook can drive hundreds of devices including microscopes, stages, lasers, wheels, piezos, scanners or shutters. It acquires data in 3D format over time, color, and specimen locations in customizable experiment protocols. This tool offers a solution to investigate images and obtain statistical data via a wide variety of algorithms while maintaining original data integrity.
Allows calculation of fluorescence resonance energy transfer (FRET) efficiencies pixel-by-pixel in microscopic images. AccPbFRET is an ImageJ plugin that enables users to correct for bleaching of the donor, for the cross-talk of the acceptor and its photoproduct to the donor channel and for partial acceptor photobleaching. The software also provides automatic registration and semi-automatic analysis of large image sets.
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