The University of California was chartered in 1868 and its flagship campus — envisioned as a "City of Learning" — was established at Berkeley, on San Francisco Bay. Today the world's premier public university and a wellspring of innovation, UC Berkeley occupies a 1,232 acre campus with a sylvan 178-acre central core. From this home its academic community makes key contributions to the economic and social well-being of the Bay Area, California, and the nation.
A Python implementation of the multistate Bennett acceptance ratio (MBAR) method for estimation of expectations and free energy differences (and their statistical uncertainties) from multiple equilibrium simulations at different thermodynamic states.
Keywords: analysis, MBAR, multistate Bennett acceptance ratio, WHAM
MSMBuilder is an open source software package for automating the construction and analysis of Markov state models (MSMs). It is primarily written in the python programming language with C extensions for the most time consuming routines. MSMs are a powerful means of modeling the structure and dynamics of molecular systems, like proteins. An MSM is essentially a map of the conformational space a molecule explores. Such models consist of a set of states and a matrix of transition probabilities (or, equivalently, transition rates) between each pair of states. Intuitively, the states in an MSM can be thought of as corresponding to local minima in the free energy landscape that ultimately determines a molecules structure and dynamics. MSMBuilder includes tools for - Constructing an MSM from a set of computer simulations (typically molecular dynamics simulations in standard formats like xtc, dcd, and pdb) - Validating statistical properties of MSMs - Mimicking various experimental protocols to allow a quantitative comparison with experiments - Driving efficient simulations via adaptive sampling (which decides where new simulations should be run to minimize statistical uncertainty in a model) The source code is available under the Downloads link to the left. Installation should take no more than 30 minutes. The video embedded below provides a more thorough introduction to the motivation for and use of MSMBuilder.
Keywords: Free energy landscape, Markov state model
This project provides code implementing the STWHAM and PTWHAM variants of the weighted histogram analysis method (WHAM) for use in the analysis of simulated and parallel tempering (or replica-exchange among temperatures) simulations.
This project provides the Matlab analysis tools for analyzing trajectory data collected from single-molecule experiments or biomolecular simulations to determine whether the observed coordinate is also a good reaction coordinate. Splitting probabilities are computed at various points along the reaction coordinate and compared to the splitting probabilities predicted from a diffusive model on the empirically observed potential of mean force, as described in the paper. Datasets and model systems described in the paper are also provided.
Keywords: data analysis, pfold, single molecule, single-molecule experiments, single-molecule pulling