fida software  (Fida Biosystems)

Journal: bioRxiv

Article Title: Screening de. novo designed protein binders in unpurified lysate using flow induced dispersion analysis

doi: 10.1101/2025.06.17.660127

Figure Lengend Snippet: (A) In FIDA, a bell-shaped peak, or Taylorgram, is produced when the fluorescently labelled molecule (indicator) reaches the detector. (B) Taylorgrams for unbound ALFA-tag indicator (in blue) and in complex with an analyte (10 µM binder 5A in red), show how the width of the peak changes upon binding.

Article Snippet: The R h values were calculated by processing the Taylorgrams using the FIDA Software v3.1 (Fida Biosystems) with a Taylorgram fraction of 75%.

Techniques: Produced, Binding Assay

Journal: bioRxiv

Article Title: Screening de. novo designed protein binders in unpurified lysate using flow induced dispersion analysis

doi: 10.1101/2025.06.17.660127

Figure Lengend Snippet: (A) Crystal structure of ALFA-tag (in cyan) in complex with the nanobody (in grey) that was used as a starting point for binder design. The ALFA-tag alone is shown on the right with the epitope residues depicted as sticks. (B) Schematic overview of the de.novo protein binder design pipeline. (C) Complexes of the ALFA-tag (in black) with the designed binders (in grey) as predicted by AlphaFold2. For each fold, only one of the ALFA-tag:binder complexes is shown as their structure is identical. (D) Apparent R h of FITC-ALFA (50 nM) when mixed with 10 µM purified binder inside the capillary (light orange). To assess the thermal stability of the binders, the binders were heated at 95°C for 5 min and FIDA measurements were performed in the same way (dark orange). An increase in R h of 10% relative to the R h obtained for FITC-ALFA alone was selected as the cutoff for binding and is indicated with a green dotted line. The green ticks highlight the positive hits. (E) Binding curves generated by representing the apparent R h of FITC-ALFA as a function of binder concentration. The solid lines correspond to the fitting to the 1:1 binding isotherm. The predicted sizes for ALFA-tag alone or in complex with the different binders are indicated in the right y-axis. All R h values correspond to mean ± SD (n = 3).

Article Snippet: The R h values were calculated by processing the Taylorgrams using the FIDA Software v3.1 (Fida Biosystems) with a Taylorgram fraction of 75%.

Techniques: Purification, Binding Assay, Generated, Concentration Assay

Journal: bioRxiv

Article Title: Screening de. novo designed protein binders in unpurified lysate using flow induced dispersion analysis

doi: 10.1101/2025.06.17.660127

Figure Lengend Snippet: (A,D) Representative gel illustrating the purity of the samples used for FIDA screening (Sol.) in either chemical (A) or heat (D) lysates separated from insoluble material (Insol.) by centrifugation. A sample with no binder expression (Neg.) and one with purified binder (Pure) were loaded for comparison. (B,E) Examples of Taylorgrams obtained when using different dilutions of chemical (B) and heat (E) lysates, evidencing the high background fluorescence associated with the lower dilutions. In B, the Taylorgram for the 2x dilution additionally shows a double peak, which is a clear signal of buffer/baseline mismatch. A higher residence time is observed for the 2x and 3x diluted heat lysates (E) likely due to the increased viscosity of the samples. (C,F) Apparent size of FITC-ALFA (200 nM) when mixed with either chemical (C) or heat (F) lysates that were diluted to different extents. A sample of preculture (PC), i.e., lacking the expressed binder, was tested to account for non-specific binding to lysate components. The values correspond to mean ± SD (n = 3). The dotted lines mark the R h of the indicator in clean buffer. The asterisks in F indicate that the samples were analysed in different days and should thus be compared to the corresponding preculture. (G) Rate of false positives in relation to the total number of binders for both lysis methods, where false positives correspond to binders that result in a 10% gain in R h relative to the preculture.

Article Snippet: The R h values were calculated by processing the Taylorgrams using the FIDA Software v3.1 (Fida Biosystems) with a Taylorgram fraction of 75%.

Techniques: Centrifugation, Expressing, Purification, Comparison, Fluorescence, Viscosity, Binding Assay, Lysis

Journal: iScience

Article Title: Rapid determination of sphingosine 1-phosphate association with carrier molecules by flow-induced dispersion analysis to predict sepsis outcome

doi: 10.1016/j.isci.2024.111168

Figure Lengend Snippet:

Article Snippet: FIDA Analysis Software , FIDA Biosystems , FIDA Software V2.32.

Techniques: Recombinant, Software, Mass Spectrometry