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From |
Joseph Coveney <jcoveney@bigplanet.com> |

To |
Statalist <statalist@hsphsun2.harvard.edu> |

Subject |
Re: st: one/two-site competitive binding ado |

Date |
Tue, 22 Apr 2003 02:32:20 +0900 |

David Airey was asking about the ability of Stata to implement nonlinear curve fitting for selected nonlinear functions of interest to pharmacologists. I had posted that Stata has -nl- and -ml- that would be helpful in this regard, and that -ml- has certain advantages, for example, the -cluster()- option. He replied, -------------------------begin excerpt from post--------------------------------- Thanks for this information. I'll likely give one of these equations a whirl to compare results. Others in the lab uses Motulsky's GraphPad prism because it's easy to use and the documentation is well done if full of typos. Be nice to have extended capabilities present in Stata that are not present in Prism. From what I can tell, Prism 3.0 has several built in (and modifiable) classic equations, such as: 1. one site binding (hyperbola) Y = Bmax * X -------- Kd + X two site binding Y = Bmax1 * X Bmax2 * X --------- + --------- Kd1 + X Kd2 + X 2. sigmoidal dose-response (top - bottom) Y = bottom + -------------------- 1 + 10^(logEC50 - X) 3. sigmoidal dose-response (variable slope) (top - bottom) Y = bottom + ------------------------------ 1 + 10^(logEC50 - X)*hillslope 4. one site competition (top - bottom) Y = bottom + -------------------- 1 + 10^(X - logEC50) 5. two site competition fraction_1 1 - fraction_1 Y = bottom + (top - bottom) *( --------------------- + -------------------- ) 1 + 10^(X-logEC50_1) 1 + 10^(X-logEC50_2) and a few others: 6. boltzmann sigmoid 7. one phase exponential decay 8. two phase exponential decay 9. one phase exponential association 10. two phase exponential association 11. exponential growth 12. power series 13. polynomial equations -------------------------end excerpt from post---------------------------------- A couple of items from the list, for example, the exponential decay and association functions (Nos. 7 through 11), might already be programmed for -nl-; there is a suite of exponential functions for -nl- that ship with Stata. It looks as if all of the functions through Number 11 would be easy to implement with -nl- if they're not already available. The last two, I believe, are currently implemented or served in various ways in Stata, for example, in -boxcox-, -fracpoly-, -boxtid- and -bspline-. In case it helps to illustrate the use of -ml- for these kinds of problems, I've programmed the first two from the list (one-site and two-site Langmuir adsorption isotherms) and attached them below in a do-file. The illustrations below use artificial datasets for a problem set exercise in a biochemistry course taught by Richard Neubig at the University of Michigan. They can be found as the first two hits from Google searching using keywords, *neubig* and *550*. (The URLs are each too long to include either on a single line here.) If there is an interest in implementing nonlinear regression items from the list above using -ml-, good references for the exercise are: 1. help for -ml-, 2. Section 3.4 "Nonlinear specifications" in W. Gould & W. Sribney, _Maximum Likelihood Estimation in Stata_ (College Station, Texas: Stata Press, 1999), pp. 44-45 [note that there's a typographical error in the code shown on Page 45--a right parenthesis is missing in each case], and 3. Chapter 13. "Maximum likelihood estimation" in S. Rabe-Hesketh & B. Everitt, _A Handbook of Statistical Analyses usng Stata_, Second Edition. (Boca Raton, Florida: Chapman & Hall/CRC, 2000), esp. pp. 181-82. Joseph Coveney -------------------------------------------------------------------------------- /* estimating receptor binding parameters at equilibrium; one binding site variables are fre (free ligand), tbn (total binding), nsb (nonspecific binding) and nbi (net or specific binding) */ clear set more off input long fre int tbn int nsb 5000 325 25 10000 550 50 20000 900 100 50000 1300 200 100000 1700 400 200000 2200 800 500000 3200 1600 end /* conversion from cpm to femtomoles */ foreach var of varlist _all { replace `var' = `var' / 0.331 / 2.22 / 136 } generate float nbi = tbn - nsb * * program define mlonesite args lnf theta1 theta2 theta3 tempvar res quietly generate double `res' = $ML_y1 - /* */ fre * `theta1'/ (`theta2' + fre) quietly replace `lnf' = -0.5 * ln(2*_pi) - /* */ ln(`theta3') - 0.5 * `res'^2 / `theta3'^2 end * * ml model lf mlonesite (Bmax:nbi=) (Kd:) (sigma:) ml check ml search ml maximize, difficult * * * /* two binding sites variables are fre (free ligand) and nbi (net or specific binding) */ clear input float fre float nbi 0.25 12.4 0.50 21.4 0.75 28.4 1.0 34.1 1.5 43 2.0 50 3.0 61 5.0 75 10 96 15 107 20 114 25 120 end aformat _all clist * * program define mltwosite args lnf theta1 theta2 theta3 theta4 theta5 tempvar res quietly generate double `res' = /* */ $ML_y1 - ( fre * `theta1'/ (`theta2' + fre) + /* */ fre * `theta3' / (`theta4' + fre) ) quietly replace `lnf' = -0.5 * ln(2*_pi) - /* */ ln(`theta5') - 0.5 * `res'^2 / `theta5'^2 end * * ml model lf mltwosite (Bmax1:nbi=) (Kd1:) (Bmax2:) (Kd2:) (sigma:) ml check ml search ml maximize, difficult exit -------------------------------------------------------------------------------- * * For searches and help try: * http://www.stata.com/support/faqs/res/findit.html * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/

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