Pre-Exascale HPC-approaches for Molecular Dynamics simulations. Covid-19 research: a use case
Exascale computing has been a dream for ages and is close to become a reality that will impact the way in which molecular simulations are being performed and the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis in recent work from groups in the BioExcel Center of Excellence for High Performance Computing.
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
Here we present the Common Workflow Language (CWL) project, which produces free and open standards for describing command-line tool based workflows. The CWL standards provide a common but reduced set of abstractions that are both used in practice and implemented in many popular workflow systems.
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) of fering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library.
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.
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.
