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Structured Review

ERITHACUS SOFTWARE LIMITED grafit5 (v.5.0.13
Grafit5 (V.5.0.13, supplied by ERITHACUS SOFTWARE LIMITED, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/grafit5/grafit+5/pmc11658767-167-12-14
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grafit5 (v.5.0.13 - by Bioz Stars, 2026-09
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Related Articles

Concentration Assay:

Article Title: Identification and analysis of novel small molecule inhibitors of RNase E: Implications for antibacterial targeting and regulation of RNase E
Article Snippet: .. To determine the half maximal inhibitory concentration (IC 50 ), data were fitted to a three-parameter IC 50 single-site inhibition model in GraFit5 (Erithacus software): y = R a n g e 1 + ( x IC 50 ) s where y is the rate of RNA cleavage determined at inhibitor concentration x ; Range is the difference between the theoretical maximal and minimal rate of RNA cleavage; IC 50 is the concentration of inhibitor at half the Range ; and s is the slope factor (a measure of how steeply the linear portion of the sigmoid falls). ..

Article Title: Structure‐Activity Relationship of NF023 Derivatives Binding to XIAP‐BIR1
Article Snippet: .. The values of fluorescence vs . inhibitor concentration were fitted with GraFit5 (Erithacus Software Limited, 2010) using the three parameters ( M, m, K d ) equation: F = M - ( M - m ) [ P T ] [ P I ] ; with [ P I ] = [ P T ] + [ I T ] + K d - ( [ P T ] + [ I T ] + K d ) 2 - 4 [ P T ] [ I T ] 2 2 where F is the fluorescence intensity, [ P T ]/[ I T ] are the total protein/inhibitor concentrations, M/m is the max/min of fluorescence and [PI] is the concentration of the protein bound to the inhibitor. ..

Article Title: An Investigation into the Potential of Targeting Escherichia coli rne mRNA with Locked Nucleic Acid (LNA) Gapmers as an Antibacterial Strategy
Article Snippet: Digitised images were quantitated using ImageJ (Rasband, W.S., ImageJ, U.S. National Institutes of Health, Bethesda, MD, USA, https://imagej.nih.gov/ij/, 1997–2018) and the percentage of bound and unbound RNA in each lane was calculated. .. Data from triplicate experiments were fit in Grafit5 (Erithacus Software, Grinstead, West Sussex, UK) to a cooperative binding equation: y = Ln.Cap Kn + [L]n + background (1) In this equation, y is the percentage of FAM-labelled RNA bound by LNA gapmer, [L] is the concentration of LNA gapmer, n is the slope factor, Cap is the theoretical maximal amount of FAM-labelled RNA than can be bound by LNA gapmer, K is the apparent equilibrium dissociation constant (also termed apparent Kd) and background allows for any y-axis displacement from the origin. ..

Inhibition:

Article Title: Identification and analysis of novel small molecule inhibitors of RNase E: Implications for antibacterial targeting and regulation of RNase E
Article Snippet: .. To determine the half maximal inhibitory concentration (IC 50 ), data were fitted to a three-parameter IC 50 single-site inhibition model in GraFit5 (Erithacus software): y = R a n g e 1 + ( x IC 50 ) s where y is the rate of RNA cleavage determined at inhibitor concentration x ; Range is the difference between the theoretical maximal and minimal rate of RNA cleavage; IC 50 is the concentration of inhibitor at half the Range ; and s is the slope factor (a measure of how steeply the linear portion of the sigmoid falls). ..

Fluorescence:

Article Title: Structure‐Activity Relationship of NF023 Derivatives Binding to XIAP‐BIR1
Article Snippet: .. The values of fluorescence vs . inhibitor concentration were fitted with GraFit5 (Erithacus Software Limited, 2010) using the three parameters ( M, m, K d ) equation: F = M - ( M - m ) [ P T ] [ P I ] ; with [ P I ] = [ P T ] + [ I T ] + K d - ( [ P T ] + [ I T ] + K d ) 2 - 4 [ P T ] [ I T ] 2 2 where F is the fluorescence intensity, [ P T ]/[ I T ] are the total protein/inhibitor concentrations, M/m is the max/min of fluorescence and [PI] is the concentration of the protein bound to the inhibitor. ..

Binding Assay:

Article Title: Characterization of a novel RP2–OSTF1 interaction and its implication for actin remodelling
Article Snippet: .. The binding affinity between RP2 and ARL3ΔN was measured by monitoring the polarization signal during titration of 1 μM ARL3 loaded with mantGppNHp with increasing amounts of RP2 in the presence or absence of 10 μM OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction using Grafit5 (Erithacus software) to obtain the dissociation constant K d . The binding affinity between OSTF1 FL and RP2 was determined indirectly by allowing formation of a complex upon incubating 1 μM ARL3 mantGppNHp with 1 μM RP2, which was titrated with increasing amounts of OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction by using Grafit5 (Erithacus software) to obtain the dissociation constant K d . ..

Article Title: Characterization of a novel RP2–OSTF1 interaction and its implication for actin remodelling
Article Snippet: .. The binding affinity between RP2 and ARL3ΔN was measured by monitoring the polarization signal during titration of 1 μM ARL3 loaded with mantGppNHp with increasing amounts of RP2 in the presence or absence of 10 μM OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction using Grafit5 (Erithacus software) to obtain the dissociation constant K d . The binding affinity between OSTF1 FL and RP2 was determined indirectly by allowing formation of a complex upon incubating 1 μM ARL3 mantGppNHp with 1 μM RP2, which was titrated with increasing amounts of OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction by using Grafit5 (Erithacus software) to obtain the dissociation constant K d . Measurement of GTP hydrolysis by [γ- 32 P]GTP charcoal method This was performed as described previously ( Veltel et al., 2008 ). .. Cells were washed in PBS prior to incubation with Alexa Fluor-conjugated goat secondary antibodies (Thermo Fisher) for a further hour at room temperature.

Article Title: An Investigation into the Potential of Targeting Escherichia coli rne mRNA with Locked Nucleic Acid (LNA) Gapmers as an Antibacterial Strategy
Article Snippet: Digitised images were quantitated using ImageJ (Rasband, W.S., ImageJ, U.S. National Institutes of Health, Bethesda, MD, USA, https://imagej.nih.gov/ij/ , 1997–2018) and the percentage of bound and unbound RNA in each lane was calculated. .. Data from triplicate experiments were fit in Grafit5 (Erithacus Software, Grinstead, West Sussex, UK) to a cooperative binding equation: (1) y = L n . C a p K n + L n + b a c k g r o u n d In this equation, y is the percentage of FAM-labelled RNA bound by LNA gapmer, [ L ] is the concentration of LNA gapmer, n is the slope factor, Cap is the theoretical maximal amount of FAM-labelled RNA than can be bound by LNA gapmer, K is the apparent equilibrium dissociation constant (also termed apparent K d ) and background allows for any y -axis displacement from the origin. .. A translational fusion of the −397 to +30 region of E. coli rne and the coding region of the firefly luciferase ( luc ) gene ( ) was synthesised by GeneArt (Thermo Fisher Scientific, Waltham, MA, USA) and ligated between the XbaI and XhoI restriction sites of pET28b (Novagen, a brand of Merck, Darmstadt, Germany) to generate pET28[ rne - luc ].

Article Title: An Investigation into the Potential of Targeting Escherichia coli rne mRNA with Locked Nucleic Acid (LNA) Gapmers as an Antibacterial Strategy
Article Snippet: Digitised images were quantitated using ImageJ (Rasband, W.S., ImageJ, U.S. National Institutes of Health, Bethesda, MD, USA, https://imagej.nih.gov/ij/, 1997–2018) and the percentage of bound and unbound RNA in each lane was calculated. .. Data from triplicate experiments were fit in Grafit5 (Erithacus Software, Grinstead, West Sussex, UK) to a cooperative binding equation: y = Ln.Cap Kn + [L]n + background (1) In this equation, y is the percentage of FAM-labelled RNA bound by LNA gapmer, [L] is the concentration of LNA gapmer, n is the slope factor, Cap is the theoretical maximal amount of FAM-labelled RNA than can be bound by LNA gapmer, K is the apparent equilibrium dissociation constant (also termed apparent Kd) and background allows for any y-axis displacement from the origin. ..

Titration:

Article Title: Characterization of a novel RP2–OSTF1 interaction and its implication for actin remodelling
Article Snippet: .. The binding affinity between RP2 and ARL3ΔN was measured by monitoring the polarization signal during titration of 1 μM ARL3 loaded with mantGppNHp with increasing amounts of RP2 in the presence or absence of 10 μM OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction using Grafit5 (Erithacus software) to obtain the dissociation constant K d . The binding affinity between OSTF1 FL and RP2 was determined indirectly by allowing formation of a complex upon incubating 1 μM ARL3 mantGppNHp with 1 μM RP2, which was titrated with increasing amounts of OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction by using Grafit5 (Erithacus software) to obtain the dissociation constant K d . ..

Article Title: Characterization of a novel RP2–OSTF1 interaction and its implication for actin remodelling
Article Snippet: .. The binding affinity between RP2 and ARL3ΔN was measured by monitoring the polarization signal during titration of 1 μM ARL3 loaded with mantGppNHp with increasing amounts of RP2 in the presence or absence of 10 μM OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction using Grafit5 (Erithacus software) to obtain the dissociation constant K d . The binding affinity between OSTF1 FL and RP2 was determined indirectly by allowing formation of a complex upon incubating 1 μM ARL3 mantGppNHp with 1 μM RP2, which was titrated with increasing amounts of OSTF1 FL at 20°C in buffer M. Obtained data points were fitted to a first-order reaction by using Grafit5 (Erithacus software) to obtain the dissociation constant K d . Measurement of GTP hydrolysis by [γ- 32 P]GTP charcoal method This was performed as described previously ( Veltel et al., 2008 ). .. Cells were washed in PBS prior to incubation with Alexa Fluor-conjugated goat secondary antibodies (Thermo Fisher) for a further hour at room temperature.

other:

Article Title: Characterization of a novel RP2–OSTF1 interaction and its implication for actin remodelling
Article Snippet: HEK293T, hTERT-RPE1 and HeLa cells were obtained from the American Type Culture Collection (ATCC) and maintained as adherent cultures at 37°C and 5% CO 2 .

Article Title: Characterization of a novel RP2–OSTF1 interaction and its implication for actin remodelling
Article Snippet: Cell culture techniques – motility, transfection and fractionation HEK293T, hTERT-RPE1 and HeLa cells were obtained from the American Type Culture Collection (ATCC) and maintained as adherent cultures at 37°C and 5% CO 2 .



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