PyCOMPSs as an instrument for Translational Computer Science
This paper describes our experience with the PyCOMPSs project, a programming model for distributed computing. While it is a research instrument for our team, it has also been applied in multiple real use cases under the umbrella of European Funded projects or as part of internal projects between various departments at the Barcelona Supercomputing Center (BSC). The paper illustrates how the authors have engaged in TCS as an underlying research methodology, collecting experiences from three European projects.
Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4
This study presents a step-by-step protocol for generating cyclic peptide conformations and docking them to their protein target using HADDOCK2.4. A dataset of 30 cyclic peptide-protein complexes was used to optimize both cyclisation and docking protocols. It supports peptides cyclized via an N- and C-terminus peptide bond and/or a disulfide bond.
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.
