Hi everybody. Are interested in this question: what software can be used to study protein thermodynamics? Which is better and which is worse. Are there any program with the ability to make changes directly in the structure itself, or for that use third-party software?
This is mostly theory:
A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
See the list of different tools in chapter 14 here:
Advances in Protein Thermodynamics, 14.
Computational Approach-Computer Simulation of Proteins for Thermodynamics and Structure Prediction
See this article for another approach:
Robust and convenient analysis of protein thermal and chemical stability
These sites may be useful as well:
COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures
Web-server for the estimation of protein stability changes upon mutation and sequence optimality