teamanandtech.org

Contributed by Stephen Goold, Voelz Lab In order for molecular simulations to make accurate predictions, it is important that we constantly evaluate the quality of protein force fields. A force field is a collection of parameters that describe all of the pairwise atomic interactions in a simulation. Many general-purpose protein force fields have been developed, and we are interested in evaluating them to see how accurate they are at predicting the conformational properties of peptides and mini-proteins in solution. To do this, we are simulating many different sequence variants of designed mini-proteins and comparing the results to experimental measurements Projects 16959 and 16974 examine a small mini-protein called Trp-cage, designed in Niels Andersen’s lab. Despite its size, Trp-case has two well-defined states: an unfolded one and a folded one, making it a great model system to understand folding mechanisms. ...

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