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.
Using machine-learning-driven approaches to boost hot-spot’s knowledge
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.
Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers
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.
A Community Roadmap for Scientific Workflows Research and Development
The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges and lay the groundwork for transforming workflows research and development, the WorkflowsRI and ExaWorks projects partnered to bring the international workflows community together.
DeepRank: A deep learning framework for data mining 3D protein-protein interfaces
Three-dimensional (3D) structures of protein complexes provide fundamental information to [...]
GA4GH: International policies and standards for data sharing across genomic research and healthcare
In this perspective, we present the GA4GH strategies for addressing the major challenges of the data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders
