Biomolecular systems possess unique, structure-encoded dynamic properties that underlie
their biological functions. Recent studies indicate that these dynamic properties are …

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 …

Abstract DynOmics (dynomics. pitt. edu) is a portal developed to leverage rapidly growing
structural proteomics data by efficiently and accurately evaluating the dynamics of …

The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring
protein dynamics. Its main utility is to predict and visualize the collective motions of large …

Elastic network models (ENMs) are entropic models that have demonstrated in many
previous studies their abilities to capture overall the important internal motions, with …

Abstract A mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode
Analysis (ENM-NMA)-based strategy (ie PSN-ENM) was developed to investigate structural …

Energy landscape theories have provided a common ground for understanding the protein
folding problem, which once seemed to be overwhelmingly complicated. At the same time …

Abstract Structure graphs, in which interacting amino acids/nucleotides correspond to linked
nodes, represent cutting-edge tools to investigate macromolecular function. The graph …

For a representative set of 64 nonhomologous proteins, each containing a structure solved
by NMR and X-ray crystallography, we analyzed the variations in atomic coordinates …

Computational modeling can provide a wealth of insight into how energy flow in proteins
mediates protein function. Computational methods can also address fundamental questions …