Pathogen-sugar interactions revealed by universal saturation transfer analysis

By |June 23, 2022|Categories: Publications|

Many pathogens exploit host cell-surface glycans. However, precise analyses of [...]

Comments Off on Pathogen-sugar interactions revealed by universal saturation transfer analysis

PyCOMPSs as an instrument for Translational Computer Science

By |June 7, 2022|Categories: Publications|Tags: , |

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.

Comments Off on PyCOMPSs as an instrument for Translational Computer Science

Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4

By |June 2, 2022|Categories: Publications|Tags: , , |

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.

Comments Off on Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4

Pre-Exascale HPC-approaches for Molecular Dynamics simulations. Covid-19 research: a use case

By |May 30, 2022|Categories: Publications|Tags: , |

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.

Comments Off on Pre-Exascale HPC-approaches for Molecular Dynamics simulations. Covid-19 research: a use case

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

By |May 20, 2022|Categories: Publications|Tags: , , |

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.

Comments Off on Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations

By |May 18, 2022|Categories: Publications|Tags: , |

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.

Comments Off on BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
Go to Top