The OPEP coarse-grained protein model has been applied to a wide range of applications
since its first release 15 years ago. The model, which combines energetic and structural …

Although RNAs play many cellular functions, little is known about the dynamics and
thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can …

HiRE-RNA is a coarse-grained model for RNA structure prediction and the dynamical study
of RNA folding. Using a reduced set of particles and detailed interactions accounting for base…

Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of
proteins and the complexes they form with other macromolecules. There are now several …

Background Normal mode analysis (NMA) using elastic network models is a reliable and
cost-effective computational method to characterise protein flexibility and by extension, their …

The volume of an internal protein pocket is fundamental to ligand accessibility. Few
programs that compute such volumes manage dynamic data from molecular dynamics (MD) …

Cryo-EM experiments produce images of macromolecular assemblies that are combined to
produce three-dimensional density maps. Typically, atomic models of the constituent …

Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires
large conformational changes, identifying rigid bodies can help optimize the model-map fit. …

Structural determination of molecular complexes by cryo-EM requires large, often complex
processing of the image data that are initially obtained. Here, TEMPy2, an update of the …

Ion mobility coupled to mass spectrometry (IM-MS) is widely used to study protein dynamics
and structure in the gas phase. Increasing the energy with which the protein ions are …