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Preclinical PKPD modeling

version 1.6.0.0 (797 KB) by Peter Gennemark
Classes for fundamental PKPD modeling in drug discovery (no support for a NLME modeling).

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Updated 03 Aug 2017

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These classes provide fundamental software modules for pharmacokinetic and pharmacodynamic (PKPD) modeling. There is no support for non-linear mixed effects (NLME) modeling. The classes may significantly facilitate implementation of tailored solutions to automate PKPD analysis (1). There are classes for representing an experiment, a dosing, observed data, and a model, as well as functions for simulating a model and for parameter estimation. There is also support for reading and writing data from/to Excel (Matlab built-in).
The classes are best explored by a couple of commented examples:
example_fit_inf: fits infusion data to a PKPD model (2-comp PK model, Emax PD model)
example_fit_ev_iv: fits extravascular (ev) and intravascular (iv) data at the same time to a 1-compartment model.
example_readExcel_PKPD_analysis: reads data from Excel file in.xlsx, performs PKPD analysis (2-comp. PK model, receptor occupancy PD model), and writes output to the Excel file.
example_fit_turnover_model: fits PK data to a 1-compartment linear model, then uses the PK parameters to fit a PKPD model (PK 1-comp + turnover model with inhibition of the loss term) to PD data (holding PK parametrs, as well as Imax and n constant).
References:
(1) Lindhardt E, Gennemark P. Automated analysis of routinely generated preclinical pharmacokinetic and pharacodynamic data. J Bioinform Comput Biol. 2014 Jun;12(3):1450010
http://www.ncbi.nlm.nih.gov/pubmed/24969748

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Updates

1.6.0.0

Three-comparment PK model, and PD turnover models added.
Steady-state analytical solutions to 1, 2 and 3-compartment models added (PK_[1,2,3]comp_Ka_Cl_fun_SS.m)
Estimation using maximum liklihood added, see example_fit_loglikelihood.m

1.5.0.0

Several new PD models (e.g. PD turnover models)
One new example
Ensured feasibility for Matlab R2014a

1.4.0.0

Added reference to published paper

1.3.0.0

PK_2comp_Ka_Cl_ode was updated.

1.2.0.0

2013-10-25: corrected calculation of coefficient of variation in Model.m. Revised example_readExcel_PKPD_writePowerPoint.m to improve readability.

MATLAB Release Compatibility
Created with R2014a
Compatible with any release
Platform Compatibility
Windows macOS Linux