README.md

In huangrenhuai/pldfit: SensorGram kinetic data fitting, especialy for BLI and SPR data

Protein-Ligand Biosensor Data Process in R

Introduction

The purpose of this package is to use R to develop novel statistic models and to fit the protein-ligand interaction data obtained from biosensor (both BLI and SPR). R is widely used in statistic analysis. R also has advantage in large data process. For example, it often takes a lot of work to read biosensor data into certain program to analysis. However, it is easy to read biosensor data into a data frame, the most common method to store data in R. In this packages, we first developed a dimerization model and applied it to fit the BLI data of von Willebrand factor propeptide. We successfully determined the dimerization constant and kinetic parameters of von Willebrand factor propeptide ( for background ) .

There are two major biosensor techniques in studying protein-ligand insteraction: Bio-layer interferometry (BLI) Surface plasmon resonance (SPR).

Model in the package: Simple one to one binding + steady state + kinetic Dimerization model: + steady state + kinetic * Multiple binding sites (to be developed) + steady state + kinetic

Other models: to request additional model, you may contact me by EMail

Installation

pldfit is developed running in R (following the link to download and install if you need). To get the currect development version from github: # require devtools > require(devtools) > devtools::install_github("huangrh/pldfit")

Model equation & simulation examples:

Equation & algotithm

Simple one to one model: simulation & fitting

Dimerization model: simulation & fitting

huangrenhuai/pldfit documentation built on May 17, 2019, 9:10 p.m.