Conspectus Protein function is inextricably linked to protein dynamics. As we move from a
static structural picture to a dynamic ensemble view of protein structure and function, novel …

As molecular dynamics (MD) simulations continue to evolve into powerful computational
tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use …

MSMBuilder is a software package for building statistical models of high-dimensional time-series
data. It is designed with a particular focus on the analysis of atomistic simulations of …

Often the analysis of time-dependent chemical and biophysical systems produces high-dimensional
time-series data for which it can be difficult to interpret which individual features are …

Osprey is a tool for hyperparameter optimization of machine learning algorithms in Python.
Hyperparameter optimization can often be an onerous process for researchers, due to …

Cell counting is a ubiquitous, yet tedious task that would greatly benefit from automation.
From basic biological questions to clinical trials, cell counts provide key quantitative feedback …

MDEntropy is a Python package for information-theoretic (IT) analysis of data generated from
molecular dynamics simulations. While correlation studies have long been of interest to the …

The field of neural networks has seen significant advances in recent years with the development
of deep and convolutional neural networks. Although many of the current works address …

MSMExplorer is a Python package for visualizing data generated from biomolecular dynamics.
While molecular visualizations have been a large focus of the molecular dynamics (MD) …

Crystallographic structures and experimental assays of human CXC chemokine receptor
type 4 (CXCR4) provide strong evidence for the capacity to homodimerize, potentially as a …