BioThermodynamics Software Available for Download

Protein Structure, Stability, and Interactions - Mathematica 6.0 Notebooks

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

Linkage - Mathematica 3.0 Notebooks

Simulating the thermodynamics of protein unfolding using protonation and anion-binding linkage relations
  • Described in Journal of Molecular Biology 276, 203-224 (1998).
  • Download linkage notebook

IgorDenat - IgorPro Procedures

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*

IgorCD - IgorPro Procedures

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*

IgorBinding - IgorPro Procedures

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