The root-mean-square deviation (RMSD) is a similarity measure widely used in analysis of
macromolecular structures and dynamics. As increasingly larger macromolecular systems …

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the
collective functional motions of biological macromolecules. iMODS facilitates the exploration …

Despite its apparent simplicity, the problem of quantifying the differences between two
structures of the same protein or complex is nontrivial and continues evolving. In this …

Markov state models provide a framework for understanding the fundamental states and
rates in the conformational dynamics of biomolecules. We describe an improved protocol for …

Visualization has been a key technology in the progress of structural molecular biology for
as long as the field has existed. This perspective describes the nature of the visualization …

SARS-CoV-2 infection across the world has led to immense turbulence in the treatment
modality, thus demanding a swift drug discovery process. Spike protein of SARS-CoV-2 …

Proteins are highly flexible molecules. Prediction of molecular flexibility aids in the
comprehension and prediction of protein function and in providing details of functional …

We have developed a method that uses energetic analysis of structure-based fragment
docking to elucidate key features for molecular recognition. This hybrid ligand-and structure …

The Community Structure–Activity Resource (CSAR) recently held its first blinded exercise
based on data provided by Abbott, Vertex, and colleagues at the University of Michigan, Ann …

Understanding how ligand binding influences protein flexibility is important, especially in
rational drug design. Protein flexibility upon ligand binding is analyzed herein using 305 …