Mathematica 9 is now available

Wolfram Library Archive


All Collections Articles Books Conference Proceedings
Courseware Demos MathSource Technical Notes
Title Downloads

Binding of Ligands to an Infinite Linear Lattice: A Model for Non-Sequence-Selective Protein-DNA Interactions
Author

Alan R. Wolfe
Organization: Dept. of Biopharmaceutical Sciences, University of California at San Francisco
Old MathSource #

0206-031
Revision date

1999-03-10
Description

These notebooks calculate and graph Scatchard plots and other relevant data (conditional probabilities, ligand orientation, cluster length distributions) for the binding of ligands to an infinite linear lattice. The ligands may be symmetric or asymmetric, and the lattice may be isotropic or anisotropic. Binding site overlap and cooperative interactions between adjacent bound ligands are taken into account. This is a mathematical model for non-sequence-selective binding of proteins and other small molecules (ligands) to a linear macromolecule such as DNA (the lattice), and is a generalization of the work of McGhee & Von Hippel, who considered the symmetric ligand, isotropic lattice case. (Our treatment of the latter case allows for the presence two different types of ligand.) The method used is described in Wolfe, A. R. & Meehan, T. (1992) J. Mol. Biol. 223, 1063-1087.
Subjects

*Science > Chemistry
*Science > Medicine
Keywords

Chemistry, Life Sciences, biology, Applied Mathematics
Downloads Download Wolfram CDF Player

Download
README.txt (15.3 KB) - Plain-text documentation for all notebooks.
Download
2L-Ex&Th-Initialize.nb (66.3 KB) - Initialization notebook for the 2 types of symmetric ligand, isotropic lattice case, experimental versus theoretical.
Download
2L-Ex&Th-Output.nb (43.2 KB) - Output notebook for the 2 types of symmetric ligand, isotropic lattice case, experimental versus theoretical.
Download
2Lig-Initialize.nb (82.8 KB) - Initialization notebook for the 2 types of symmetric ligand, isotropic lattice case, theoretical only.
Download
2Lig-Output.nb (29.3 KB) - Output notebook for the 2 types of symmetric ligand, isotropic lattice case, theoretical only.
Download
Ani-Initialize.nb (215.6 KB) - Initialization notebook for the asymmetric ligand, anisotropic lattice case.
Download
Ani-Output.nb (45.7 KB) - Output notebook for the asymmetric ligand, anisotropic lattice case.
Download
Iso-Initialize.nb (95.5 KB) - Initialization notebook for the asymmetric ligand, isotropic lattice case.
Download
Iso-Output.nb (37.6 KB) - Output notebook for the asymmetric ligand, isotropic lattice case.
Download
README.nb (28.8 KB) - Mathematica notebook documentation for all notebooks.
Download
Sym-Initialize.nb (49.4 KB) - Initialization notebook for the symmetric ligand case.
Download
Sym-Output.nb (34.6 KB) - Output notebook for for the symmetric ligand case.
Download
schema&derivation.nb (520.9 KB) - Mathematica notebook

Files specific to Mathematica 2.2 version:
Download
README.txt (11.4 KB) - Plain-text documentation for all notebooks
Download
2Lig-Initialize.ma (37.2 KB) - Initialization notebook for 2Lig-Output.ma
Download
2Lig-Output.ma (14.9 KB) - Notebook for symmetric ligands of 2 types on an isotropic lattice
Download
Ani-Initialize.ma (99.7 KB) - Initialization notebook for Ani-Output.ma
Download
Ani-Output.ma (19.1 KB) - Notebook for asymmetric ligands on an anisotropic lattice
Download
Iso-Initialize.ma (43.2 KB) - Initialization notebook for Iso-Output.ma
Download
Iso-Output.ma (16 KB) - Notebook for asymmetric ligands on an isotropic lattice
Download
README.ma (15.6 KB) - Mathematica notebook documentation for all notebooks
Download
Sym-Initialize.ma (21 KB) - Initialization notebook for Sym-Output.ma
Download
Sym-Output.ma (13.6 KB) - Notebook for symmetric ligands of 1 type