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.

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Evolutionary Path and Host-selection Mechanism of SARS-CoV-2

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

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.

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DNAffinity: A machine-learning approach to predict DNA binding affinities of transcription factors

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

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.

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The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization

By |May 16, 2022|Categories: Publications|Tags: , , , |

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.

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BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools

By |May 11, 2022|Categories: Publications|Tags: , |

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.

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Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel

By |May 6, 2022|Categories: Publications|Tags: , , , |

Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in [...]

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