Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

The ATSAS software suite encompasses a number of programs for the processing,
visualization, analysis and modelling of small-angle scattering data, with a focus on the data …

Motivation After the outstanding breakthrough of AlphaFold in predicting protein 3D models,
new questions appeared and remain unanswered. The ensemble nature of proteins, for …

It has become commonplace to employ principal component analysis to reveal the most
important motions in proteins. This method is more commonly known by its acronym, PCA …

The assembly of individual proteins into functional complexes is fundamental to nearly all
biological processes. In recent decades, many thousands of homomeric and heteromeric …

Although algebraic graph theory-based models have been widely applied in physical
modeling and molecular studies, they are typically incompetent in the analysis and …

The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …

Crystallography supplies unparalleled detail on structural information critical for mechanistic
analyses; however, it is restricted to describing low energy conformations of …

A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …