DNAffinity: A machine-learning approach to predict DNA binding affinities of transcription factors
We present a physics-based machine learning approach to predict transcription factor binding affinities in vitro from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations.
The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization
Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail.
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools
BioBB REST API extends and complements the BioBB library offering programmatic access to the collection of biomolecular simulation tools included in the BioExcel Building Blocks library. Molecular Dynamics setup, docking, structure modeling, free energy simulations, and flexibility analyses are examples of functionalities included in the endpoints collection. All functionalities are accessible through standard REST API calls, voiding the need for tool installation.
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in [...]
Prediction Of The Impact Of Genetic Variability On Drug Sensitivity For Clinically Relevant EGFR Mutations
Mutations in the kinase domain of the Epidermal Growth Factor [...]
Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion [...]
