BioExcel Whitepaper on Scientific Software Development (BioExcel-2 update)
This white paper presents the experience of the developers and recommendations for development of high-quality software engineering processes.
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design
We assess costs and efficiency of state-of-the-art high-performance cloud computing [...]
Ten Simple Rules for making a software tool workflow-ready
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
Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine
Voltage-gated potassium channels of the Kv7.x family are involved in [...]
Making Canonical Workflow Building Blocks interoperable across workflow languages
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.
Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
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.
