Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

We present a method to predict complex structural (conformational) transitions in irregular or
disordered macromolecular systems, such as proteins or glasses, at the atomic level. Our …

Titin, an important constituent of vertebrate muscles, is a protein of the order of a micrometer
in length in the folded state. Atomic force microscopy and laser tweezer experiments have …

The present computational power and sophistication of theoretical approaches to nucleic
acid structural investigation are sufficient for the realization of static and dynamic models that …

The computational sampling of rare, large-scale, conformational transitions in proteins is a
well appreciated challenge—for which a number of potentially efficient path-sampling …

The vibrational dynamics of transfer RNAs, both free, and complexed with the cognate
synthetase, are analyzed using a model (Gaussian network model) which recently proved to …

Coarse-grained models can be very different from all-atom models and are highly varied.
Each class of model is assembled very differently, and some models need customized …

Integrins are composed of noncovalently bound dimers of an α‐and a β‐subunit. They play
an important role in cell‐matrix adhesion and signal transduction through the cell …

The normal mode analysis of human hemoglobin showed the presence in the deoxy T-state
of one main preferential direction that brings the structure close to the R-state, with a low …

Conformational transitions in proteins provide the mechanism for enacting many critical
biological functions at the molecular level. Unfortunately, a full description of the ensemble …