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Use the ",{"type":25,"tag":182,"props":835,"children":837},{"href":836},"/tools/residual-plot",[838],{"type":31,"value":839},"Residual Plot Generator",{"type":31,"value":841}," to check the adequacy of any fitted kinetic model by examining model residuals.",{"type":25,"tag":26,"props":843,"children":845},{"id":844},"frequently-asked-questions",[846],{"type":31,"value":847},"Frequently Asked Questions",{"type":25,"tag":34,"props":849,"children":850},{},[851,856,858,862,864,869,871,876,878,883,885,890],{"type":25,"tag":38,"props":852,"children":853},{},[854],{"type":31,"value":855},"How do I decide which kinetic model to use before fitting?",{"type":31,"value":857},"\nStart by plotting V vs ",{"type":25,"tag":60,"props":859,"children":860},{},[861],{"type":31,"value":64},{"type":31,"value":863}," on a regular scale. If the curve is ",{"type":25,"tag":38,"props":865,"children":866},{},[867],{"type":31,"value":868},"hyperbolic and levels off",{"type":31,"value":870}," → Michaelis-Menten. If it is ",{"type":25,"tag":38,"props":872,"children":873},{},[874],{"type":31,"value":875},"S-shaped",{"type":31,"value":877}," → Hill equation. If it ",{"type":25,"tag":38,"props":879,"children":880},{},[881],{"type":31,"value":882},"rises then falls",{"type":31,"value":884}," → substrate inhibition. Then, if you have inhibitor data, create a Lineweaver-Burk plot and look at the intersection pattern of inhibited vs uninhibited lines to select the inhibition model. The AI can do this diagnosis automatically if you ask it to ",{"type":25,"tag":166,"props":886,"children":887},{},[888],{"type":31,"value":889},"\"test all inhibition models and select the best fit by AIC\"",{"type":31,"value":891},".",{"type":25,"tag":34,"props":893,"children":894},{},[895,900,902,907],{"type":25,"tag":38,"props":896,"children":897},{},[898],{"type":31,"value":899},"What units should my data be in?",{"type":31,"value":901},"\nAny consistent units work — the AI will carry them through. Common conventions: substrate in µM or mM, time in minutes or seconds, rate in µmol/min, nmol/min, or absorbance units/min. For kcat calculation you also need enzyme concentration in matching molar units. Describe your units in the prompt: ",{"type":25,"tag":166,"props":903,"children":904},{},[905],{"type":31,"value":906},"\"substrate in µM, rate in nmol/min per mg protein, enzyme is 5 nM\"",{"type":31,"value":891},{"type":25,"tag":34,"props":909,"children":910},{},[911,916,918,923,925,930],{"type":25,"tag":38,"props":912,"children":913},{},[914],{"type":31,"value":915},"My Km value changed dramatically with a mutation — is that a Km or kcat effect?",{"type":31,"value":917},"\nBoth can change with mutations. Always report ",{"type":25,"tag":38,"props":919,"children":920},{},[921],{"type":31,"value":922},"kcat and kcat/Km",{"type":31,"value":924}," alongside Km. If Km increases but kcat stays constant, the mutation impairs substrate binding (binding site mutation). If kcat decreases but Km stays constant, the mutation impairs catalysis (active site mutation). If both change, ask the AI to ",{"type":25,"tag":166,"props":926,"children":927},{},[928],{"type":31,"value":929},"\"fit MM for WT and mutant; report Km, Vmax, kcat, and kcat/Km with 95% CI for each\"",{"type":31,"value":891},{"type":25,"tag":34,"props":932,"children":933},{},[934,939,941,952,954,965],{"type":25,"tag":38,"props":935,"children":936},{},[937],{"type":31,"value":938},"How do I estimate Ki from dose-response inhibition data (not initial rate data)?",{"type":31,"value":940},"\nThe Cheng-Prusoff equation converts IC50 to Ki: ",{"type":25,"tag":38,"props":942,"children":943},{},[944,946,950],{"type":31,"value":945},"Ki = IC50 / (1 + ",{"type":25,"tag":60,"props":947,"children":948},{},[949],{"type":31,"value":64},{"type":31,"value":951},"/Km)",{"type":31,"value":953},". Ask the AI to ",{"type":25,"tag":166,"props":955,"children":956},{},[957,959,963],{"type":31,"value":958},"\"use the Cheng-Prusoff equation: IC50 = 15 µM, ",{"type":25,"tag":60,"props":960,"children":961},{},[962],{"type":31,"value":64},{"type":31,"value":964}," = 20 µM, Km = 10 µM — calculate Ki\"",{"type":31,"value":966},". This requires knowing the Km and the substrate concentration used in the assay. For a full IC50-to-Ki conversion with confidence intervals, also provide the Hill coefficient from the dose-response fit.",{"type":25,"tag":34,"props":968,"children":969},{},[970,975,977,982],{"type":25,"tag":38,"props":971,"children":972},{},[973],{"type":31,"value":974},"Can I analyze progress curves rather than initial rates?",{"type":31,"value":976},"\nYes — progress curve analysis fits a differential equation model directly to the full time course, extracting Km and kcat without requiring initial rate measurement. Ask the AI to ",{"type":25,"tag":166,"props":978,"children":979},{},[980],{"type":31,"value":981},"\"fit integrated Michaelis-Menten to progress curve data; columns 'time_s' and 'product_uM'; report Km and kcat\"",{"type":31,"value":983},". This is especially useful when substrate concentrations are too low to measure initial rates accurately.",{"title":7,"searchDepth":985,"depth":985,"links":986},2,[987,988,989,990,991,992,993,994],{"id":28,"depth":985,"text":32},{"id":116,"depth":985,"text":119},{"id":208,"depth":985,"text":211},{"id":460,"depth":985,"text":463},{"id":603,"depth":985,"text":606},{"id":733,"depth":985,"text":736},{"id":801,"depth":985,"text":804},{"id":844,"depth":985,"text":847},"markdown","content:tools:038.enzyme-kinetics-fit.md","content","tools/038.enzyme-kinetics-fit.md","tools/038.enzyme-kinetics-fit","md",{"loc":4},1775502468197]