Explicit solvent Folding@home trajectories for Aurora A kinase (AurA) from our Nature Chemical Biology paper
Soreen Cyphers, Emily F Ruff, Julie M Behr, John D Chodera, and Nicholas M Levinson.
A water-mediated allosteric network governs activation of Aurora kinase A
Nature Chemical Biology, in press. [DOI] [GitHub]
We have made all the explicit-solvent Folding@home simulation data and analysis scripts used in this paper available for download:
The trajectory data itself is too large to share via GitHub, so we make it available via the Open Science Framework.
A microsecond trajectory of the human tyrosine kinase ABL1 kinase domain generated on Foldign@home using the OpenMM 6.3 core (core 21).
Ensembler-generated Tyrosine kinase models
Solvated alanine dipeptide - thermodynamics and kinetics
A collection of datasets of the alanine dipeptide (more specifically, terminally-blocked alanine peptide) in explicit solvent. These datasets cover both thermodynamic simulations (parallel tempering) and kinetic simulations (Hamiltonian dynamics trajectories) useful for testing algorithms analyzing the thermodynamics and kinetics of biomolecular systems. This model system has already been used in several research papers.
Laboratory automation system data feeds
Human kinome bacterial expression data
Cyclohexane / water distribution coefficients for the SAMPL5 challenge
For the purpose of the SAMPL5 distribution coefficient challenge, 53 small-molecule cyclohexane/water distribution coefficients have been measured at Genentech as part of an internship project. The data set is publicly available on Github, including the scripts used to analyze the results.