This morning, Christian submitted a great pull request to speed up YAML parsing in MSMBuilder using LibYAML. In MSMBuilder, we use a YAML file to save the "project", which is keeps the path to all of the files associated with an MSMBuilder project, such as the different trajectories, and a ...

A few weeks ago, I gave the Pande Group meeting. The slides are on github, and you can view them here. The title of the talk is Protein Folding is Easy: Towards Markov State Models for Conformational Change, and mostly addresses my learning distance metrics for kinetic clustering of protein ...

One of the goals of the MSMBuilder3 development is to make the package as easy to use as possible. Analyzing molecular dynamics is hard enough, so there's no reason that the software should get in your way.

Currently, all of the the MSMBuilder commands are separate scripts that are ...