BioThermodynamics Software Available for Download

Simulating thermodynamics and ligand binding linkage

Described in "Protein Structure, Stability, and Interactions", Methods in Molecular Biology, Springer Protocols, Hamana Press, Ed., Shriver, 2008.
Protein Folding Notebook - melts and DSC
Stability of Multimeric Proteins Notebook
Binding and Linkage Notebook - A (simple binding)
Binding and Linkage Notebook - B (T and ITC)
Binding and Linkage Notebook - C (linkage)
Download binding/linkage notebooks

Simulating the thermodynamics of protein unfolding using protonation and anion-binding linkage relations

Thermal and Chemical Denaturation Analysis Software (ver 3.x)

Igor Pro procedures for analyzing protein unfolding data
differential scanning calorimetry (DSC), spectroscopic thermal melts, and chemical denaturation (LEM and denaturant binding models)
Includes 5 selectable models of protein unfolding:
N <-> U (simple 2-state unfolding model)
N <-> I <-> U (3-state unfolding)
D <-> 2U (dimer 2-state unfolding model
D <-> 2I <-> 2U (3-state dimer unfolding)
D <-> I <-> 2U (alternate 3-state dimer unfolding)
3-state models can be linked termodynamically or treated as independent
allows for simulation and curve fitting using control panel interface
facilitates global fitting of multiple data sets
For screen shots of version 2, click here and here
Download version 3.xx *updated November, 2010*

Circular Dichroism Processing Software

Igor Pro routines for processing spectra with emphasis on CD spectra, but useful for absorption also
does it the way I think it should be done, not the manufacturer of the instrument.
features include: tab delimited Excel-type text file import, data smoothing, baseline subtraction, correct for baseline shifts, operate on a series of spectra automatically, extract melting/titration curves from multidimensional data, convert data to delta epsilon units, multicomponent analysis, etc.
for description of package with screen shot click here
Download version 2.x * updated August, 2011*

Binding Analysis Software

designed primarily for DNA-protein binding but can also be used for ligand-protein binding
can be used for both forward and reverse titrations
used for both spectroscopic titrations and ITC
6 different models of McGhee-vonHipple DNA-protein binding: polymer DNA, oligonucleotide, specific & nonspecific competing, specific & flanking nonspecific, polymer DNA with 2 binding modes, same but 2nd mode is cooperative dimer
also includes single-site binding model and Hill equation
allows for simulation and curve fitting using control panel interface
Download binding/titration procedures

Alabama High Field NMR Center