data
Computational Datasets
Explicit solvent Folding@home trajectories for Aurora A kinase (AurA) from our Nature Chemical Biology paper
Authors: Soreen Cyphers, Emily F. Ruff, Julie M. Behr, John D. Chodera, and Nicholas M. Levinson
Description: We have made all the explicit-solvent Folding@home simulation data and analysis scripts used in this paper available for download: here
Citation: Cyphers, Soreen, et al. A water-mediated allosteric network governs activation of Aurora kinase A. Nature chemical biology 13.4 (2017): 402-408. https://doi.org/10.1038/nchembio.2296
Link to dataset: https://osf.io/afg8h/
Microsecond trajectory of human tyrosine kinase ABL1 kinase domain on Figshare
Authors: Sonya Hanson and John D. Chodera
Description: A microsecond trajectory of the human tyrosine kinase ABL1 kinase domain generated on Foldign@home using the OpenMM 6.3 core (core 21).
Citation: Chodera, John; Hanson, Sonya (2016). Microsecond molecular dynamics simulation of kinase domain of the human tyrosine kinase ABL1. figshare. Dataset.
Link to dataset: https://dx.doi.org/10.6084/m9.figshare.4496795.v1
Ensembler-generated Tyrosine kinase models
Authors: Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle A. Beauchamp, and John D. Chodera
Description: A collection of structures of all human tyrosine kinase catalytic domains modeled onto all kinase domain structures from any organism from the RCSB using our Ensembler, high-throughput modeling and simulation setup tool.
Citation: Parton, Daniel L.; Grinaway, Patrick B.; Hanson, Sonya M. et al. (2017). Data from: Ensembler: enabling high-throughput molecular simulations at the superfamily scale [Dataset]. Dryad. https://doi.org/10.5061/dryad.7fg32
Link to dataset: http://dx.doi.org/10.5061/dryad.7fg32
Solvated alanine dipeptide - thermodynamics and kinetics
Authors: John D. Chodera, Nina Singhal, Vijay S. Pande, Ken A. Dill, and William C. Swope
Description: 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.
Citation: Chodera, John D., et al. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. The Journal of chemical physics 126.15 (2007). https://doi.org/10.1063/1.2714538
Link to dataset: https://simtk.org/home/alanine-dipeptide/
Experimental Datasets
Human kinome bacterial expression data
Authors: Steven K. Albanese, Daniel L. Parton, Mehtap Işık, Lucelenie Rodríguez-Laureano, Sonya M. Hanson, Julie M. Behr, Scott Gradia, Chris Jeans, Nicholas M. Levinson, Markus A. Seeliger, John D. Chodera
Description: Constructs of human kinase domains known to express well in E. coli, using the PDB as a source of potential expression constructs, confirmed by automated cloning and expression.
Citation: Albanese, Steven K., et al. An open library of human kinase domain constructs for automated bacterial expression. Biochemistry 57.31 (2018): 4675-4689. https://doi.org/10.1063/1.2714538
Plasmids available via Addgene https://www.addgene.org/kits/chodera-kinase-domains.
Link to dataset: http://choderalab.github.io/kinome-data/kinase_constructs-addgene_hip_sgc.html
Cyclohexane / water distribution coefficients for the SAMPL5 challenge
Authors: Bas Rustenburg, John D. Chodera, David L. Mobley
Description: 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.
Link to dataset: https://github.com/choderalab/sampl5-experimental-logd-data