Ten Simple Rules for making a software tool workflow-ready

By |March 24, 2022|Categories: Publications|Tags: , , |

There is little specific guidance for writing software intended to slot in as a tool within a workflow; or on converting an existing standalone research-quality software tool into a reusable, composable, well-behaved citizen within a larger workflow. In this paper we present 10 simple rules for how a software tool can be prepared for workflow use

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Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine

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

Voltage-gated potassium channels of the Kv7.x family are involved in [...]

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Making Canonical Workflow Building Blocks interoperable across workflow languages

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

We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms.

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Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

By |February 22, 2022|Categories: Publications|

Nowadays, drug design projects benefit from highly accurate protein–ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects.

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Using machine-learning-driven approaches to boost hot-spot’s knowledge

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

This review aims to present the current knowledge on PPIs, providing a detailed understanding of the microspecifications of the residues involved in those interactions and the characteristics of those defined as HS through a thorough assessment of related field-specific methodologies.

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Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

By |January 13, 2022|Categories: Publications|Tags: , , |

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design.

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