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

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 …

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Exploring the landscape of large scale conformational changes such as protein folding at
atomistic detail poses a considerable computational challenge. Coarse-grained …

Computational studies of large macromolecular assemblages have come a long way during
the past 10 years. With the explosion of computer power and parallel computing, timescales …

The large number of available HIV-1 protease structures provides a remarkable sampling of
conformations of the different conformational states, which can be viewed as direct structural …

Normal mode analysis (NMA) is a technique that can be used to describe the flexible states
accessible to a protein about an equilibrium position. These states have been shown …

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 …

Normal mode analysis is a computational technique that allows to study the dynamics of
biological macromolecules. It was first applied to small protein cases, more than thirty years …