On the linkage of thermodynamics and pathogenicity

P Pandey, S Ghimire, B Wu, E Alexov - Current opinion in structural biology, 2023 - Elsevier
This review outlines the effect of disease-causing mutations on proteins' thermodynamics.
Two major thermodynamics quantities, which are essential for structural integrity, the folding …

Structural perspective on revealing and altering molecular functions of genetic variants linked with diseases

Y Peng, E Alexov, S Basu - International journal of molecular sciences, 2019 - mdpi.com
Structural information of biological macromolecules is crucial and necessary to deliver
predictions about the effects of mutations—whether polymorphic or deleterious (ie, disease …

Predicting the effect of single mutations on protein stability and binding with respect to types of mutations

P Pandey, SK Panday, P Rimal, N Ancona… - International Journal of …, 2023 - mdpi.com
The development of methods and algorithms to predict the effect of mutations on protein
stability, protein–protein interaction, and protein–DNA/RNA binding is necessitated by the …

ProTherm: thermodynamic database for proteins and mutants

MM Gromiha, J An, H Kono, M Oobatake… - Nucleic acids …, 1999 - academic.oup.com
The first release of the Thermodynamic Database for Proteins and Mutants (ProTherm)
contains more than 3300 data of several thermodynamic parameters for wild type and …

On the physics of thermal-stability changes upon mutations of a protein

S Murakami, H Oshima, T Hayashi… - The Journal of chemical …, 2015 - pubs.aip.org
It is of great interest from both scientific and practical viewpoints to theoretically predict the
thermal-stability changes upon mutations of a protein. However, such a prediction is an …

Lower kinetic limit to protein thermal stability: a proposal regarding protein stability in vivo and its relation with misfolding diseases

IM Plaza del Pino, B Ibarra‐Molero… - Proteins: Structure …, 2000 - Wiley Online Library
In vitro thermal denaturation experiments suggest that, because of the possibility of
irreversible alterations, thermodynamic stability (ie, a positive value for the unfolding Gibbs …

Decomposition of the free energy of a system in terms of specific interactions: implications for theoretical and experimental studies

AE Mark, WF Van Gunsteren - Journal of molecular biology, 1994 - Elsevier
Recently, a number of methods have been proposed that are designed to extract
contributions to the change in free energy associated with a given perturbation or mutation …

The linear interaction energy method for the prediction of protein stability changes upon mutation

L Wickstrom, E Gallicchio… - … : Structure, Function, and …, 2012 - Wiley Online Library
The coupling of protein energetics and sequence changes is a critical aspect of
computational protein design, as well as for the understanding of protein evolution, human …

Free energy perturbation calculations of the thermodynamics of protein side-chain mutations

T Steinbrecher, R Abel, A Clark, R Friesner - Journal of Molecular Biology, 2017 - Elsevier
Protein side-chain mutation is fundamental both to natural evolutionary processes and to the
engineering of protein therapeutics, which constitute an increasing fraction of important …

Most monogenic disorders are caused by mutations altering protein folding free energy

P Pandey, E Alexov - International Journal of Molecular Sciences, 2024 - mdpi.com
Revealing the molecular effect that pathogenic missense mutations have on the
corresponding protein is crucial for developing therapeutic solutions. This is especially …