The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows
Developing complex biomolecular workflows is not always straightforward. It requires [...]
Automated relative binding free energy calculations: from SMILES to ΔΔG
In drug discovery, computational methods are a key part of [...]
Best practices in constant pH MD simulations: accuracy and sampling
Various approaches have been proposed to include the effect of [...]
Evolutionary Path and Host-selection Mechanism of SARS-CoV-2
Here, through massive plain MD simulations, enhanced sampling calculations, free energy-based alchemical transformation and bioinformatics we show that SARS-CoV-2 likely evolved in Rhinolophus affinis bats by acquiring a surprisingly-high affinity for their ACE2 receptors.
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.
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 [...]
