In this review, we summarize the computational methods for sampling the conformational
space of biomacromolecules. We discuss the methods applicable to find only lowest energy …

The conformational fluctuations of proteins can be described using structural ensembles. To
address the challenge of determining these ensembles accurately, a wide range of …

Protein folding and protein–ligand docking have long persisted as important subjects in
biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic …

Flexible polypeptides such as unfolded proteins may access an astronomical number of
conformations. The most advanced simulations of such states usually comprise tens of …

Proteins are dynamic molecules that can transition between a potentially wide range of
structures comprising their conformational ensemble. The nature of these conformations and …

Abstract We describe a Bayesian/Maximum entropy (BME) procedure and software to
construct a conformational ensemble of a biomolecular system by integrating molecular …

A comparison study has been carried out to test the relative efficiency of Metropolis Monte
Carlo and molecular dynamics simulations for conformational sampling. The test case that …

The prediction of protein structure from sequence remains a major unsolved problem in
biology. The most successful protein structure prediction methods make use of a divide-and …

Many proteins consist of folded domains connected by regions with higher flexibility. The
details of the resulting conformational ensemble play a central role in controlling interactions …

Proteins exert a variety of fascinating functions to participate in virtually all cellular
processes. Underlying these highly controlled activities are the ordered conformational …